p9310s  (New England Biolabs)

Journal: bioRxiv

Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

doi: 10.64898/2026.04.30.722071

Figure Lengend Snippet: (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.

Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

Techniques: Modification, Generated, RNA Sequencing, Binding Assay

Journal: bioRxiv

Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

doi: 10.64898/2026.04.30.722071

Figure Lengend Snippet: (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.

Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

Techniques: Binding Assay, RNA Sequencing, Control, Hi-C

Journal: bioRxiv

Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

doi: 10.64898/2026.04.30.722071

Figure Lengend Snippet: (A) Heatmap showing averaged z-scored enrichment of CUT&RUN reads from all three lamin isoforms (lamin), histone modification CUT&RUN (H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me3), and ATAC-seq signal across the six HiLands chromatin states of YSE cells. Lamin enrichment was calculated as fold-change over IgG CUT&RUN prior to z-scoring; histone modification CUT&RUN and ATAC-seq enrichment was z-scored directly. (B) Representative genomic region showing the six HiLands in wild-type YSE cells with genome browser tracks of LADs determined by lamin CUT&RUN enrichment compared to IgG CUT&RUN, histone modification CUT&RUN, and ATAC-seq. Boxed regions highlight fragmented LADs characterized by HiLands-G and -Y. (C) Alluvial plot showing transitions of HiLands-P and HiLands-B LADs in mESCs to their corresponding HiLands in YSE cells. (D) Schematic illustration of the four categories of LADs and non-LADs in mESCs and YSE cells. (E) Representative genomic region illustrating the four categories of LADs and non-LADs in mESCs and YSE cells. Genome browser tracks include published mESC HiLands and LADs mapped by lamin-B1 Dam-ID, as well as hidden-Markov model (HMM)-called mESC LAD annotations generated in this study. Additional tracks include YSE HiLands, YSE HMM-called LAD annotations, and YSE LADs mapped by lamin CUT&RUN all generated in this study. Dashed boxes indicate examples of YSE-specific non-LADs, shared LADs, YSE-specific LAD regions, and shared non-LADs. (F) Representative fragmented YSE-specific LAD regions (dashed boxes). Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, H3K27ac CUT&RUN, and H3K27me3 CUT&RUN generated in this study. (G) Zoomed-in view of the gray highlighted region in (F) showing an example expressed YSE gene involved in lipid metabolism within HiLands-R and a repressed broad-lineage gene within HiLands-O regions that interrupt YSE-specific LADs. Genome browser tracks include YSE HiLands, ATAC-seq, RNA-seq, as well as H3K27ac and H3K27me3 CUT&RUN generated in this study. (H) Representative YSE-specific non-LAD (dashed boxed) containing the highly expressed YSE gene Afp . Genome browser tracks include published mESC LADs mapped by lamin-B1 Dam-ID and HiLands, along with YSE HiLands, LADs mapped by lamin CUT&RUN, ATAC-seq, and RNA-seq generated in this study. (I) Enrichment of binding motifs for YSE-relevant transcription factors in YSE ATAC-seq peaks associated with shared LADs, YSE-specific non-LADs, and YSE-specific LAD regions.

Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

Techniques: Modification, Generated, RNA Sequencing, Binding Assay

Journal: bioRxiv

Article Title: Lamins and lineage-relevant transcription factors coordinate gene expression in lineage development

doi: 10.64898/2026.04.30.722071

Figure Lengend Snippet: (A and B) Metaplots of H3K27ac CUT&RUN signal around promoters of downregulated genes associated with binding motifs of YSE-relevant transcription factors (A) and H3K27me3 CUT&RUN signal around promoters of upregulated genes associated with binding motifs of YSE-relevant transcriptions (B) in the indicated LAD and non-LAD regions. (C) Genome browser view of ATAC-seq peaks and GATA4/6 binding motifs around the upregulated broad-lineage gene Cxcl12 , alongside tracks of bulk RNA-seq and H3K27me3 CUT&RUN from control and lamin-A/B1 DKO cells. An ATAC-seq peak containing GATA4/6 motifs is highlighted (dashed box). (D) Heatmap showing 3D chromatin interaction changes around Cxcl12 upon lamin-A/B1 loss. Boxed regions and arrows highlight increased interactions with transcriptionally active HiLands-R and reduced interactions with repressive HiLands-B. (E) Genome browser view of ATAC-seq and HNF4α binding motifs around the downregulated gene Afp with known functions in YSE cells, alongside tracks of bulk RNA-seq and H3K27ac CUT&RUN from control and lamin-A/B1 DKO cells. ATAC-seq peaks containing HNF4α motifs are highlighted (dashed box). (F) Heatmap showing 3D chromatin interaction changes around Afp upon lamin-A/B1 loss. Boxed regions and arrows indicate increased interactions with repressive HiLands-B. (G and H) Heatmaps of observed/expected (O/E) Hi-C interactions of the zoomed-in region around Afp outlined by the dashed box in (F) of control (G) and lamin-A/B1 DKO (H) YSE cells. The boxed region and arrows highlight reduced interactions between Afp and transcriptionally active HiLands-R upon lamin-A/B1 loss.

Article Snippet: The following antibodies were used for additional CUT&RUN: Lamin-A/C (Abcam, ab133256), Lamin-B1 (Abcam, ab16048), Lamin-B2 (Abcam, ab138516), H3K9me2 (Diagenode, C15200154), H3K9me3 (Active Motif, Cat. no. 39062), H3K27ac (Epicypher, 13–0059), H3K27me3 (Epicypher, 13-0055).

Techniques: Binding Assay, RNA Sequencing, Control, Hi-C