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gal4 reporter luc hek293 recombinant cell line bps bioscience  (BPS Bioscience)


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    BPS Bioscience gal4 reporter luc hek293 recombinant cell line bps bioscience
    Gal4 Reporter Luc Hek293 Recombinant Cell Line Bps Bioscience, supplied by BPS Bioscience, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/gal4+reporter+luc+hek293+recombinant+cell+line+bps+bioscience/GAL4+Reporter+(Luc)-HEK293+Recombinant+Cell+Line/pm33894155-281-203-209
    Average 91 stars, based on 1 article reviews
    gal4 reporter luc hek293 recombinant cell line bps bioscience - by Bioz Stars, 2026-09
    91/100 stars

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    Sequencing:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Modification:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Reverse Transcription:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Bradford Assay:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    SYBR Green Assay:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Polymerase Chain Reaction:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Imaging:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1

    Recombinant:

    Article Title: A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-C1QBP antibody Cell Signaling Cat#5734; RRID: AB_10831050 Anti-FLAG antibody Sigma-Aldrich Cat#F1804; RRID: AB_262044 Anti-H3 antibody Cell Signaling Cat#9715; RRID: AB_331563 Anti-H4 antibody Cell Signaling Cat#13919; RRID: AB_2798345 Anti-H2B antibody Cell Signaling Cat#2934; RRID: AB_2295301 Anti-tubulin antibody Abcam Cat#ab6160; RRID: AB_305328 Anti-HSP60 antibody Cell Signaling Cat#4870; RRID: AB_2295614 Anti-Lamin A/C antibody Cell Signaling Cat#4777; RRID: AB_10545756 Bacterial and Virus Strains MAX Efficiency DH5a Competent Cells Thermo Fisher Scientific Cat#18258012 Rosetta (DE3) Competent Cells Novagen Cat#70954 Chemicals, peptides, and recombinant proteins Ethyl acetoacetate Sigma-Aldrich Cat#537349 2,2-Dimethyl-1,3-propanediol TCI Cat#D0791 Phosphorus pentasulfide Sigma-Aldrich Cat#232106 Boc-Cys-OH Sigma-Aldrich Cat#8.53031 Fmoc protected amino acids GL Biochem N/A Rink Amide-MBHA Resin GL Biochem Cat#49101 Fmoc-ADdis-Cys This paper N/A cOmplete EDTA-Free Protease Inhibitor Cocktail Roche Cat#04693132001 TBTA Click Chemistry Tools Cat#1061-500 DADPS Biotin Azide Click Chemistry Tools Cat#1330 Pierce High-capacity streptavidin agarose Thermo Fisher Scientific Cat#20361 Zeba Spin Desalting Column with 7K MWCO Thermo Fisher Scientific Cat#89893 H3K4cr: H2N-ART Kcr QTARKSTGGKA-COOH This paper N/A H3K4me3: H2N-ART Kme3 QTARKSTGGKA-COOH This paper N/A Probe I: H2N-ART Kme3 QT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe II: H2N-ART Kcr QT ADdis-Cys RKS-CONH2 This paper N/A Probe III: H2N-GKGGAKRHR Kme2 V ADdis-Cys RDNIQGIT-CONH2 This paper N/A Probe IV: H2N-TSRHK Kme1 L ADdis-Cys FK-CONH2 This paper N/A Probe V: H2N-IPKRRT ADdis-Cys R Kme3 QLPK-CONH2 This paper N/A Probe VI: H2N-ARTKQT ADdis-Cys RKSTGG Kac A-CONH2 This paper N/A Probe VII: H2N-ARTKQTARKSTGG Kac A ADdis-Cys RKQ-CONH2 This paper N/A (Continued on next page) e1 Molecular Cell 81, 1–13.e1–e9, June 17, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Probe C1: H2N-ARTKQT ADdis-Cys RKSTGGKA-CONH2 This paper N/A Probe C2: H2N-GKGGAKRHRKV ADdisCys RDNIQGIT-CONH2 This paper N/A Probe C3: H2N-TSRHKKL ADdis-Cys FK-CONH2 This paper N/A Probe C4: H2N-IPKRRT ADdis-Cys RKQLPK-CONH2 This paper N/A GST-SPIN1 This paper N/A GST-ING2 (208-270) This paper N/A GST-MORC3 (400-461) This paper N/A GST-WDR5 This paper N/A GST-L3MBTL1 (206-519) This paper N/A SIRT3 (102-399)-His6 This paper N/A C1QBP (74-282, L74M) This paper N/A GST-ZMYND8 (75-402) This paper N/A UHRF1-His6 This paper N/A Histone H2A This paper N/A Histone H2B This paper N/A Histone H3 This paper N/A Histone H4 This paper N/A Sequencing grade modified trypsin Promega Cat#V5111 Proteinase K Thermo Fisher Scientific Cat#25530049 RNase A Thermo Fisher Scientific Cat#12091021 SuperScript IV Reverse Transcriptase Thermo Fisher Scientific Cat#18090200 Critical commercial assays Bradford assay kit Bio-Rad Cat#500-0006 QIAprep Spin Miniprep Kit QIAGEN Cat#27104 Phanta Max Super-Fidelity DNA Polymerase Vazyme Cat#P505 Power SYBR Green PCR Master Mix Thermo Fisher Scientific Cat#4367659 Pierce Firefly Luc One-Step Glow Assay Kit Thermo Fisher Scientific Cat#16197 Deposited data Raw Imaging Files This study, Mendeley Data https://doi.org/10.17632/6hzvtywynb.1 Experimental models: Cell lines HeLa cell line ATCC Cat#CCL-2 HeLa S3 cell line ATCC Cat#CCL-2.2 HEK293T cell line ATCC Cat#CRL-11268 U2OS cell line ATCC Cat# GAL4 reporter (Luc)-HEK293 recombinant cell line BPS Bioscience Cat60656 Oligonucleotides Luc-ChIP-F: 50-GAAGGGCCCAGCGCCATTCTAC-30 IDT N/A Luc-ChIP-R: 50-GTCGGTAAAGGCGATGGTGCCG-30 IDT N/A Widom-601-F: 50- GTGCGGCCGCCATCGAGAATCCCGG-30 IDT N/A (Continued on next page) Molecular Cell 81, 1–13.e1–e9, June 17, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Widom-601-R:50ATCTTACGCGCATCGGATGTATATATC-30 IDT N/A Recombinant DNA pCMV-3xflag-C1QBP This paper N/A pET3a-C1QBP (74-282, L74M) This paper N/A pGEX-6P-1-SPIN1 Yang et al., 2015 N/A pGEX-6P-1-ING2 (208-270) Yang et al., 2015 N/A pDEST15-MORC3 (400-461) Yang et al., 2015 N/A pGEX-6P-1-WDR5 Gift from Nancy Jennifer N/A pTricHis-SIRT3 (102-399) Gift from Eric Verdin N/A pGEX-6P-1-ZMYND8 (75-402) Gift from M. G. Lee N/A pGEX-6P-1-L3MBTL1 (206-519) Gift from Haitao Li N/A pETM13-UHRF1 Gift from Wolfgang Fischle N/A pET-histone expression plasmids Gift from Bing Zhu N/A Software and algorithms GraphPad prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ Maxquant Cox Group https://www.maxquant.org/ ImageJ NIH https://imagej.nih.gov/ij/ Xcalibur Thermo Fisher Scientific N/A T-coffee T-coffee http://tcoffee.crg.cat/ Jalview Jalview https://www.jalview.org/ PDV Zhang Lab http://pdv.zhang-lab.org/ Other Detailed Protocol This paper Methods S1



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