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For: Engelen E, Brandsma JH, Moen MJ, Signorile L, Dekkers DHW, Demmers J, Kockx CEM, Ozgür Z, van IJcken WFJ, van den Berg DLC, Poot RA. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat Commun 2015;6:7155. [PMID: 25990348 PMCID: PMC4455091 DOI: 10.1038/ncomms8155] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 04/13/2015] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
1
Del Burgo FG, García-López MÁ, Pons T, de Luis EV, Martínez-A C, Villares R. The chromatin reader Dido3 is a regulator of the gene network that controls B cell differentiation. Cell Biosci 2025;15:56. [PMID: 40287726 PMCID: PMC12034202 DOI: 10.1186/s13578-025-01394-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 04/11/2025] [Indexed: 04/29/2025]  Open
2
Kougnassoukou Tchara PE, Loehr J, Lambert JP. Coupling Proximity Biotinylation with Genomic Targeting to Characterize Locus-Specific Changes in Chromatin Environments. J Proteome Res 2025;24:1845-1860. [PMID: 40054857 PMCID: PMC11976867 DOI: 10.1021/acs.jproteome.4c00931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 02/16/2025] [Accepted: 02/26/2025] [Indexed: 04/05/2025]
3
Marzano S, Pinto G, Di Porzio A, Amato J, Randazzo A, Amoresano A, Pagano B. Identifying G-quadruplex-interacting proteins in cancer-related gene promoters. Commun Chem 2025;8:64. [PMID: 40025218 PMCID: PMC11873050 DOI: 10.1038/s42004-025-01462-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 02/20/2025] [Indexed: 03/04/2025]  Open
4
Wang Y, Fan J, Meng X, Shu Q, Wu Y, Chu GC, Ji R, Ye Y, Wu X, Shi J, Deng H, Liu L, Li YM. Development of nucleus-targeted histone-tail-based photoaffinity probes to profile the epigenetic interactome in native cells. Nat Commun 2025;16:415. [PMID: 39762271 PMCID: PMC11704063 DOI: 10.1038/s41467-024-55046-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/26/2024] [Indexed: 01/11/2025]  Open
5
Takemon Y, Pleasance ED, Gagliardi A, Hughes CS, Csizmok V, Wee K, Trinh DL, Huff RD, Mungall AJ, Moore RA, Chuah E, Mungall KL, Lewis E, Nelson J, Lim HJ, Renouf DJ, Jones SJ, Laskin J, Marra MA. Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities. Genome Med 2024;16:136. [PMID: 39578878 PMCID: PMC11583415 DOI: 10.1186/s13073-024-01401-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 10/29/2024] [Indexed: 11/24/2024]  Open
6
Rusling DA, Vasquez KM. A third strand for protein-DNA interactions. Nat Chem 2024;16:1748-1750. [PMID: 39406977 PMCID: PMC11671174 DOI: 10.1038/s41557-024-01652-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2024]
7
Demaili A, Portugalov A, Maroun M, Akirav I, Braun K, Bock J. Early life stress induces decreased expression of CB1R and FAAH and epigenetic changes in the medial prefrontal cortex of male rats. Front Cell Neurosci 2024;18:1474992. [PMID: 39503008 PMCID: PMC11534599 DOI: 10.3389/fncel.2024.1474992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 10/07/2024] [Indexed: 11/08/2024]  Open
8
Jiang L, Li Y, Gu Y, Zheng J, Wei L, Wei M, Zou J, Wei C, Mo B, Pan L, Zhao L, Wang D. Identification of the Beta Subunit Fas1p of Fatty Acid Synthetase as an Interacting Partner of Yeast Calcium/Calmodulin-Dependent Protein Kinase Cmk2p Through Mass Spectrometry Analysis. Appl Biochem Biotechnol 2024;196:6836-6848. [PMID: 38411936 DOI: 10.1007/s12010-024-04891-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
9
Chervova A, Molliex A, Baymaz HI, Coux RX, Papadopoulou T, Mueller F, Hercul E, Fournier D, Dubois A, Gaiani N, Beli P, Festuccia N, Navarro P. Mitotic bookmarking redundancy by nuclear receptors in pluripotent cells. Nat Struct Mol Biol 2024;31:513-522. [PMID: 38196033 PMCID: PMC10948359 DOI: 10.1038/s41594-023-01195-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
10
Shi T, Bai Y, Wu X, Wang Y, Iqbal S, Tan W, Ni Z, Gao Z. PmAGAMOUS recruits polycomb protein PmLHP1 to regulate single-pistil morphogenesis in Japanese apricot. PLANT PHYSIOLOGY 2023;193:466-482. [PMID: 37204822 DOI: 10.1093/plphys/kiad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
11
Sun Z, Lin Y, Islam MT, Koche R, Hedehus L, Liu D, Huang C, Vierbuchen T, Sawyers CL, Helin K. Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1. Mol Cell 2023;83:2398-2416.e12. [PMID: 37402365 PMCID: PMC10529604 DOI: 10.1016/j.molcel.2023.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/27/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023]
12
Nickel GA, Diehl KL. Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications. ACS Chem Biol 2023;18:1014-1026. [PMID: 35238546 PMCID: PMC9440160 DOI: 10.1021/acschembio.1c00794] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
13
Qin F, Li B, Wang H, Ma S, Li J, Liu S, Kong L, Zheng H, Zhu R, Han Y, Yang M, Li K, Ji X, Chen PR. Linking chromatin acylation mark-defined proteome and genome in living cells. Cell 2023;186:1066-1085.e36. [PMID: 36868209 DOI: 10.1016/j.cell.2023.02.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/01/2022] [Accepted: 02/02/2023] [Indexed: 03/05/2023]
14
Investigation of SAMD1 ablation in mice. Sci Rep 2023;13:3000. [PMID: 36810619 PMCID: PMC9944271 DOI: 10.1038/s41598-023-29779-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023]  Open
15
Mammary-Enriched Transcription Factors Synergize to Activate the Wap Super-Enhancer for Mammary Gland Development. Int J Mol Sci 2022;23:ijms231911680. [PMID: 36232979 PMCID: PMC9569684 DOI: 10.3390/ijms231911680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022]  Open
16
Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells. Tissue Cell 2022;78:101893. [DOI: 10.1016/j.tice.2022.101893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/28/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022]
17
A chemical method for genome- and proteome-wide enrichment and O-GlcNAcylation profiling of chromatin-associated proteins. Talanta 2022;241:123167. [DOI: 10.1016/j.talanta.2021.123167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
18
Kikutake C, Suyama M. Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis. Cancer Med 2022;11:3902-3916. [PMID: 35416406 PMCID: PMC9582691 DOI: 10.1002/cam4.4749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/11/2022]  Open
19
An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping. Int J Mol Sci 2022;23:ijms23042260. [PMID: 35216376 PMCID: PMC8878802 DOI: 10.3390/ijms23042260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022]  Open
20
Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021;15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022]  Open
21
Yu S, Zhang R, Shen Q, Zhu Z, Zhang J, Wu X, Zhao W, Li N, Yang F, Wei H, Hua J. ESRRB Facilitates the Conversion of Trophoblast-Like Stem Cells From Induced Pluripotent Stem Cells by Directly Regulating CDX2. Front Cell Dev Biol 2021;9:712224. [PMID: 34616727 PMCID: PMC8488167 DOI: 10.3389/fcell.2021.712224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022]  Open
22
Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res 2021;31:1663-1679. [PMID: 34426512 PMCID: PMC8415381 DOI: 10.1101/gr.275472.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
23
Tong Y, Zhang S, Riddle S, Zhang L, Song R, Yue D. Intrauterine Hypoxia and Epigenetic Programming in Lung Development and Disease. Biomedicines 2021;9:944. [PMID: 34440150 PMCID: PMC8394854 DOI: 10.3390/biomedicines9080944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]  Open
24
Zhang X, Spiegel J, Martínez Cuesta S, Adhikari S, Balasubramanian S. Chemical profiling of DNA G-quadruplex-interacting proteins in live cells. Nat Chem 2021;13:626-633. [PMID: 34183817 PMCID: PMC8245323 DOI: 10.1038/s41557-021-00736-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022]
25
Stielow B, Simon C, Liefke R. Making fundamental scientific discoveries by combining information from literature, databases, and computational tools - An example. Comput Struct Biotechnol J 2021;19:3027-3033. [PMID: 34136100 PMCID: PMC8175269 DOI: 10.1016/j.csbj.2021.04.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/18/2022]  Open
26
Cozzolino F, Iacobucci I, Monaco V, Monti M. Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era. J Proteome Res 2021;20:3018-3030. [PMID: 33961438 PMCID: PMC8280749 DOI: 10.1021/acs.jproteome.1c00074] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
27
Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. SCIENCE ADVANCES 2021;7:7/20/eabf2229. [PMID: 33980486 PMCID: PMC8115922 DOI: 10.1126/sciadv.abf2229] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/25/2021] [Indexed: 05/06/2023]
28
van Mierlo G, Vermeulen M. Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities. Mol Cell Proteomics 2021;20:100056. [PMID: 33556626 PMCID: PMC7973309 DOI: 10.1074/mcp.r120.002208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
29
Greenberg MVC. Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Front Cell Dev Biol 2021;8:629068. [PMID: 33490089 PMCID: PMC7817772 DOI: 10.3389/fcell.2020.629068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]  Open
30
Li H, Long C, Xiang J, Liang P, Li X, Zuo Y. Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region. Brief Bioinform 2020;22:6034044. [PMID: 33316032 DOI: 10.1093/bib/bbaa342] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]  Open
31
Mitra A, Raicu AM, Hickey SL, Pile LA, Arnosti DN. Soft repression: Subtle transcriptional regulation with global impact. Bioessays 2020;43:e2000231. [PMID: 33215731 PMCID: PMC9068271 DOI: 10.1002/bies.202000231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022]
32
Eckersley-Maslin MA, Parry A, Blotenburg M, Krueger C, Ito Y, Franklin VNR, Narita M, D'Santos CS, Reik W. Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment. Nat Struct Mol Biol 2020;27:696-705. [PMID: 32572255 PMCID: PMC7614975 DOI: 10.1038/s41594-020-0443-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
33
Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol 2020;27:706-716. [DOI: 10.1038/s41594-020-0445-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
34
In situ chromatin interactomics using a chemical bait and trap approach. Nat Chem 2020;12:520-527. [PMID: 32472103 DOI: 10.1038/s41557-020-0474-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
35
Kim M, Lin S. Characterization of histone modification patterns and prediction of novel promoters using functional principal component analysis. PLoS One 2020;15:e0233630. [PMID: 32459819 PMCID: PMC7252632 DOI: 10.1371/journal.pone.0233630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/08/2020] [Indexed: 12/04/2022]  Open
36
Lloyd SM, Bao X. Pinpointing the Genomic Localizations of Chromatin-Associated Proteins: The Yesterday, Today, and Tomorrow of ChIP-seq. ACTA ACUST UNITED AC 2020;84:e89. [PMID: 31483109 DOI: 10.1002/cpcb.89] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
37
Purification and enrichment of specific chromatin loci. Nat Methods 2020;17:380-389. [PMID: 32152500 DOI: 10.1038/s41592-020-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
38
Cuevas-Bermúdez A, Garrido-Godino AI, Gutiérrez-Santiago F, Navarro F. A Yeast Chromatin-enriched Fractions Purification Approach, yChEFs, from Saccharomyces cerevisiae. Bio Protoc 2020;10:e3471. [PMID: 33654706 DOI: 10.21769/bioprotoc.3471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 11/02/2022]  Open
39
Guthmann M, Burton A, Torres‐Padilla M. Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep 2019;20:e47952. [PMID: 31701657 PMCID: PMC6893284 DOI: 10.15252/embr.201947952] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022]  Open
40
Agbo L, Lambert JP. Proteomics contribution to the elucidation of the steroid hormone receptors functions. J Steroid Biochem Mol Biol 2019;192:105387. [PMID: 31173874 DOI: 10.1016/j.jsbmb.2019.105387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
41
Cuevas-Bermúdez A, Garrido-Godino AI, Navarro F. A novel yeast chromatin-enriched fractions purification approach, yChEFs, for the chromatin-associated protein analysis used for chromatin-associated and RNA-dependent chromatin-associated proteome studies from Saccharomyces cerevisiae. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Rahe DP, Hobert O. Restriction of Cellular Plasticity of Differentiated Cells Mediated by Chromatin Modifiers, Transcription Factors and Protein Kinases. G3 (BETHESDA, MD.) 2019;9:2287-2302. [PMID: 31088904 PMCID: PMC6643894 DOI: 10.1534/g3.119.400328] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/11/2019] [Indexed: 12/30/2022]
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Gerovska D, Araúzo-Bravo MJ. Computational analysis of single-cell transcriptomics data elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo. Sci Rep 2019;9:8930. [PMID: 31222057 PMCID: PMC6586892 DOI: 10.1038/s41598-019-45438-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/06/2019] [Indexed: 01/05/2023]  Open
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Yan YL, Zhang C, Hao J, Wang XL, Ming J, Mi L, Na J, Hu X, Wang Y. DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program. PLoS Biol 2019;17:e3000324. [PMID: 31226106 PMCID: PMC6608977 DOI: 10.1371/journal.pbio.3000324] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 07/03/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]  Open
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De Iaco A, Coudray A, Duc J, Trono D. DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells. EMBO Rep 2019;20:embr.201847382. [PMID: 30948459 PMCID: PMC6500978 DOI: 10.15252/embr.201847382] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 11/30/2022]  Open
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Trinkle-Mulcahy L. Recent advances in proximity-based labeling methods for interactome mapping. F1000Res 2019;8:F1000 Faculty Rev-135. [PMID: 30774936 PMCID: PMC6357996 DOI: 10.12688/f1000research.16903.1] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/23/2019] [Indexed: 02/03/2023]  Open
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Eckersley-Maslin M, Alda-Catalinas C, Blotenburg M, Kreibich E, Krueger C, Reik W. Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program. Genes Dev 2019;33:194-208. [PMID: 30692203 PMCID: PMC6362816 DOI: 10.1101/gad.321174.118] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2023]
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Singh AA, Schuurman K, Nevedomskaya E, Stelloo S, Linder S, Droog M, Kim Y, Sanders J, van der Poel H, Bergman AM, Wessels LF, Zwart W. Optimized ChIP-seq method facilitates transcription factor profiling in human tumors. Life Sci Alliance 2018;2:e201800115. [PMID: 30620009 PMCID: PMC6311467 DOI: 10.26508/lsa.201800115] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 01/27/2023]  Open
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Levernæs MCS, Brandtzaeg OK, Amundsen SF, Reubsaet L, Lundanes E, Halvorsen TG, Wilson SR. Selective Fishing for Peptides with Antibody-Immobilized Acrylate Monoliths, Coupled Online with NanoLC-MS. Anal Chem 2018;90:13860-13866. [DOI: 10.1021/acs.analchem.8b00935] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Klein RH, Tung PY, Somanath P, Fehling HJ, Knoepfler PS. Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. Stem Cell Res 2018;31:83-94. [PMID: 30031967 PMCID: PMC6133722 DOI: 10.1016/j.scr.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022]  Open
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