Literature DB >> 32152500

Purification and enrichment of specific chromatin loci.

Mathilde Gauchier1, Guido van Mierlo2, Michiel Vermeulen3, Jérôme Déjardin4.   

Abstract

Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.

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Year:  2020        PMID： 32152500     DOI： 10.1038/s41592-020-0765-4

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  63 in total

1.  Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes.

Authors:  Hisham Mohammed; Christopher Taylor; Gordon D Brown; Evaggelia K Papachristou; Jason S Carroll; Clive S D'Santos
Journal:  Nat Protoc       Date:  2016-01-21       Impact factor: 13.491

2.  High-resolution profiling of histone methylations in the human genome.

Authors:  Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Dustin E Schones; Zhibin Wang; Gang Wei; Iouri Chepelev; Keji Zhao
Journal:  Cell       Date:  2007-05-18       Impact factor: 41.582

3.  A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements.

Authors:  Gerhard Mittler; Falk Butter; Matthias Mann
Journal:  Genome Res       Date:  2008-11-17       Impact factor: 9.043

4.  Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions.

Authors:  Xiong Ji; Daniel B Dadon; Brian J Abraham; Tong Ihn Lee; Rudolf Jaenisch; James E Bradner; Richard A Young
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-09       Impact factor: 11.205

5.  Affinity purification of sequence-specific DNA binding proteins.

Authors:  J T Kadonaga; R Tjian
Journal:  Proc Natl Acad Sci U S A       Date:  1986-08       Impact factor: 11.205

6.  Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers.

Authors:  Michiel Vermeulen; H Christian Eberl; Filomena Matarese; Hendrik Marks; Sergei Denissov; Falk Butter; Kenneth K Lee; Jesper V Olsen; Anthony A Hyman; Henk G Stunnenberg; Matthias Mann
Journal:  Cell       Date:  2010-09-17       Impact factor: 41.582

7.  An Oct4-centered protein interaction network in embryonic stem cells.

Authors:  Debbie L C van den Berg; Tim Snoek; Nick P Mullin; Adam Yates; Karel Bezstarosti; Jeroen Demmers; Ian Chambers; Raymond A Poot
Journal:  Cell Stem Cell       Date:  2010-04-02       Impact factor: 24.633

8.  Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry.

Authors:  Erik Engelen; Johannes H Brandsma; Maaike J Moen; Luca Signorile; Dick H W Dekkers; Jeroen Demmers; Christel E M Kockx; Zehila Ozgür; Wilfred F J van IJcken; Debbie L C van den Berg; Raymond A Poot
Journal:  Nat Commun       Date:  2015-05-20       Impact factor: 14.919

9.  Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins.

Authors:  Mahmoud-Reza Rafiee; Charles Girardot; Gianluca Sigismondo; Jeroen Krijgsveld
Journal:  Mol Cell       Date:  2016-10-20       Impact factor: 17.970

10.  Nucleosome-interacting proteins regulated by DNA and histone methylation.

Authors:  Till Bartke; Michiel Vermeulen; Blerta Xhemalce; Samuel C Robson; Matthias Mann; Tony Kouzarides
Journal:  Cell       Date:  2010-10-29       Impact factor: 41.582
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  7 in total

1.  Catchet-MS identifies IKZF1-targeting thalidomide analogues as novel HIV-1 latency reversal agents.

Authors:  Enrico Ne; Raquel Crespo; Ray Izquierdo-Lara; Shringar Rao; Selin Koçer; Alicja Górska; Thomas van Staveren; Tsung Wai Kan; David van de Vijver; Dick Dekkers; Casper Rokx; Panagiotis Moulos; Pantelis Hatzis; Robert-Jan Palstra; Jeroen Demmers; Tokameh Mahmoudi
Journal:  Nucleic Acids Res       Date:  2022-06-10       Impact factor: 19.160

2.  Epi-Decoder: Decoding the Local Proteome of a Genomic Locus by Massive Parallel Chromatin Immunoprecipitation Combined with DNA-Barcode Sequencing.

Authors:  Maria Elize van Breugel; Fred van Leeuwen
Journal:  Methods Mol Biol       Date:  2022

3.  Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia.

Authors:  Jonathan D Lee; Joao A Paulo; Ryan R Posey; Vera Mugoni; Nikki R Kong; Giulia Cheloni; Yu-Ru Lee; Frank J Slack; Daniel G Tenen; John G Clohessy; Steven P Gygi; Pier Paolo Pandolfi
Journal:  Nat Methods       Date:  2021-03-01       Impact factor: 28.547

Review 4.  Mechanisms of enhancer action: the known and the unknown.

Authors:  Anil Panigrahi; Bert W O'Malley
Journal:  Genome Biol       Date:  2021-04-15       Impact factor: 13.583

5.  Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs.

Authors:  Satoru Ide; Asuka Sasaki; Yusuke Kawamoto; Toshikazu Bando; Hiroshi Sugiyama; Kazuhiro Maeshima
Journal:  Epigenetics Chromatin       Date:  2021-10-09       Impact factor: 4.954

Review 6.  Applications of CRISPR-Cas Technologies to Proteomics.

Authors:  Georgii Dolgalev; Ekaterina Poverennaya
Journal:  Genes (Basel)       Date:  2021-11-12       Impact factor: 4.096

7.  aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin.

Authors:  Georgios C Stefos; Eszter Szantai; Dimitris Konstantopoulos; Martina Samiotaki; Maria Fousteri
Journal:  Nucleic Acids Res       Date:  2021-06-21       Impact factor: 16.971
  7 in total

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