Polymerase Chain Reaction:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Gel Extraction:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
RNA Extraction:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
cDNA Synthesis:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Bicinchoninic Acid Protein Assay:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Multiplex Assay:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Chromatin Immunoprecipitation:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
RNA Sequencing:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Hi-C:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
shRNA:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Quantitative RT-PCR:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Fluorescence In Situ Hybridization:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
Recombinant:Article Title: Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-Cas9 (S.pyogenes) CST Cat#14697;RRID: AB_2750916 Rabbit polyclonal anti-β-Actin CST Cat#4967;RRID: AB_330288 Rabbit monoclonal anti-GAPDH CST Cat#2118;RRID: AB_561053 Rabbit polyclonal anti-FXN Abcam Cat#ab175402;RRID: AB_2935904 Rabbit polyclonal anti-GFP Abcam Cat#ab290;RRID: AB_303395 Rabbit polyclonal anti-RAD21 Abcam Cat#ab992;RRID: AB_2176601 Mouse monoclonal anti-RAD21 Millipore Cat#05-908;RRID: AB_11214315 Rabbit polyclonal anti-Histone 3 Abcam Cat#ab1791;RRID: AB_302613 Rabbit monoclonal anti-CTCF CST Cat#3418;RRID: AB_2086791 Rabbit monoclonal anti-SMC3 CST Cat#5696;RRID: AB_10705575 Rabbit monoclonal anti-RBMX CST Cat#14794;RRID: AB_2798614 Mouse monoclonal anti-NIPBL SCBT Cat#sc374625;RRID: AB_10989775 Mouse monoclonal anti-WAPL SCBT Cat#sc365189;RRID: AB_10708870 Mouse monoclonal anti-hnRNPL SCBT Cat#sc32317;RRID: AB_627736 Rabbit polyclonal anti-LaminB1 Abcam Cat#16048;RRID: AB_443298 Rabbit polyclonal anti-H3K9me2 Active Motif Cat#39239;RRID: AB_2793199 Mouse monoclonal anti-OCT4 Millipore Cat#MAB4419;RRID: AB_1977399 Mouse monoclonal anti-LaminAC SCBT Cat#sc376248;RRID: AB_10991536 Goat anti-Rabbit IgG (H+L) AF488 Thermo FIsher Cat#A32731;RRID: AB_2633280 Goat anti-Mouse IgG (H+L) AF488 Thermo FIsher Cat#A10680;RRID: AB_2534062 Goat anti-Rabbit IgG (H+L) AF555 Thermo FIsher Cat#A32732;RRID: AB_2633281 Goat anti-Mouse IgG (H+L) AF555 Thermo FIsher Cat#A32727;RRID: AB_2633276 Goat anti-Rabbit IgG (HRP-linked) CST Cat#7074;RRID: AB_2099233 Horse anti-Mouse IgG (HRP-linked) CST Cat#7076;RRID: AB_330924 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) NEB Cat#C3040 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11965084 Fetal Bovine Serum Cytiva Cat#SH30910.03 Penicillin-Streptomycin Thermo Fisher Cat#15140122 Non-Essential Amino Acids Thermo Fisher Cat#11140050 TripLE Express Gibco Cat#12604021 Matrigel Sigma Cat#CLS356234 Essential 8 Medium Thermo Fisher Cat#A1517001 EDTA Invitrogen Cat#15575020 Thiazovinin Cayman Chemical Cat#14245-10 McCoy’s 5A (Modified) Media Gibco Cat#166000082 5-Ph-IAA MedChemExpress Cat#HY-134653 Lipofectamine 2000 Invitrogen Cat#11668019 PowerUp SYBR Green Master Mix Thermo Fisher Cat#A25742 DMSO Sigma Cat#D2650 Triptolide CST Cat#97539 Protein G Magnetic Beads Invitrogen Cat#10004D (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Bovine Serum Albumin Sigma Cat#A4503 DAPI Sigma Cat#D9542 SlowFade Antifade Mountant Invitrogen Cat#S36936 SSC Invitrogen Cat#15557036 Formamide Thermo Fisher Cat#BP227500 Dextran Sulfate Thermo Fisher Cat#BP1585 dNTPs Invitrogen Cat#18427088 RNase OUT Invitrogen Cat#1077019 TetraSpeck Fluorescent Beads Invitrogen Cat#T7279 Glucose Oxidase Sigma Cat#G2133 Catalase Sigma Cat#C3556 Q5 High-Fidelity Master Mix NEB Cat#0492 NEBuilder HiFi DNA Assembly Master Mix NEB Cat#2621 Critical commercial assays Expand High Fidelity PCR System Roche Cat#0473825001 QIAquick Gel Extraction Kit Qiagen Cat#28704 RNeasy Total RNA Extraction Kit Qiagen Cat#74106 iScript cDNA Synthesis Kit BioRad Cat#1708891 BCA Protein Assay Kit Thermo Fisher Cat#23225 NEBNext Ultra II DNA Library Prep Kit NEB Cat#E7770L NEBNext Multiplex Oligos NEB CatE7630 NEBNext Library Quant Kit NEB Cat#E7630 Deposited data LMNB1/H3K9me2/RAD21 ChIP-seq in HCT116/human fibroblasts This study GEO: GSE266505 LMNB1 DamID in HCT116 https://data.4dnucleome.org/ 4DNES24XA7U8 LMNB1 DamID in HFFc6 https://data.4dnucleome.org/ 4DNESXZ4FW4T RNA-seq in HFFc6 https://data.4dnucleome.org/ 4DNESFH3EHTU Micro-C data in HFFc6 https://data.4dnucleome.org/ 4DNESWST3UBH Hi-C data in HFFc6 https://data.4dnucleome.org/ 4DNESN49VY8X Chromatin Interaction data in HCT116 https://www.ncbi.nlm.nih.gov/geo GEO: GSE279166 ATAC-seq in HFFc6 https://data.4dnucleome.org/ 4DNESMBA9T3L Experimental models: Cell lines Human NTC fibroblasts Robert B. Wilson Lab N/A Human FRDA fibroblasts Robert B. Wilson Lab N/A HCT116 ATCC Cat#CCL-247;RRID: CVCL+0291 RAD21-mAID-HCT116 Masato Kanemaki Lab N/A LentiX-HEK293t ATCC Cat#CRL-1573;RRID: CVCL_0045 Human FRDA corrected iPSC Marek Napierala Lab N/A Human FRDA iPSC Marek Napierala Lab N/A Oligonucleotides shRNA oligonucleotides, see Data S1 This study N/A qRT-PCR primers, see Data S1 This study N/A gRNA sequences, see Data S1 This study N/A FISH probe sequences, see Data S1 This study N/A Recombinant DNA Lenti-(BB)-EF1a-KRAB-dCas9-P2A-BlastR Addgene Cat#118154 EF1a-NLS-dCas9-VP64-2A-Blast-WPRE Addgene Cat#61425 (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 86, 1–20.e1–e11, May 21, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLV-U6-gRNA-UbC-eGFP-P2A-Bsr Addgene Cat#83925 pLenti-(BB)-EF1a-KRAB-Y46AdCas9-P2A-BlastR This study N/A pLenti-SpBsmBI-sgRNA-Hygro Addgene Cat#62205 pLenti-dCas9-EGFP-Blast This study N/A pLJM1-Smc3 This study N/A pLJM1-Smc3_K38A This study N/A SGEP-shFXN This study N/A SGEP-shNTC This study N/A pLKO.1-puro-shNIPBL This study N/A pLKO.1-puro-shWAPL This study N/A pLKO.1-puro-shCTCF This study N/A pLKO.1-puro-RAD21 This study N/A psPAX2 Addgene Cat#12260 pMD2.G Addgene Cat#12259 Software and algorithms Leica Lightning Process Deconvolution v3.5.6.21594 Leica https://www.leica-microsystems.com/products/ microscope-software/p/leica-las-x-ls/ NimOS NanoimagerTM Software v1.7.210222-3a3ef15d ONI https://oni.bio/nanoimager/ Imaris 8.1.2 Oxford Instruments https://imaris.oxinst.com MATLAB vR2020a Mathworks https://www.mathworks.com/ products/matlab.html Prism 10 GraphPad https://www.graphpad.com bcl2fastq2 v2.20 Illumina https://support.illumina.com/sequencing/ sequencing_software/bcl2fastq-conversionsoftware.html Bowtie 2 v2.5.1 Langmead Lab / Johns Hopkins University https://bowtie-bio.sourceforge.net/bowtie2/ fastp v0.23.2 OpenGene https://github.com/OpenGene/fastp sambamba v1.0.0 Sambamba project https://github.com/biod/sambamba deepTools v3.5.1 Max Planck Institute for Immunobiology and Epigenetics https://deeptools.readthedocs.io/ MACS2 v2.2.6 MACS project https://github.com/macs3-project/MACS pyGenomeTracks v3.8 pyGenomeTracks project https://pygenometracks.readthedocs.io/ FastQC v0.12.1 Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ eulerr v7.0.2 CRAN / R Project https://cran.r-project.org/package=eulerr BEDTools v2.30.0 Quinlan Lab / University of Utah https://bedtools.readthedocs.io/ BEDOPS v2.4.41 BEDOPS project https://bedops.readthedocs.io/ samtools v1.16.1 SAMtools / HTSlib project https://www.htslib.org/ Intervene v0.6.5 Intervene project https://intervene.readthedocs.io/ R v4.3.2 R Project for Statistical Computing https://www.r-project.org/ ggplot2 v3.4.4 tidyverse https://ggplot2.tidyverse.org/ ComplexHeatmap v2.20.0 Bioconductor https://bioconductor.org/packages/ ComplexHeatmap/ MultiQC v1.33 Seqera https://docs.seqera.io/multiqc/ featureCounts v2.1.1 Subread project https://subread.sourceforge.net/ featureCounts.html DESeq2 v1.50.2 Bioconductor https://bioconductor.org/packages/DESeq2/ (Continued on next page) ll OPEN ACCESSArticle Molecular Cell 86, 1–20.e1–e11, May 21, 2026 e3
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