Literature DB >> 22183598

Reconstitution of modified chromatin templates for in vitro functional assays.

Miyong Yun1, Chun Ruan, Jae-Wan Huh, Bing Li.   

Abstract

To study the functions of histone modifications in the context of chromatin, it is necessary to be able to prepare nucleosomal templates that carry specific posttranslational modifications in a defined biochemical system. Here, we describe two sets of protocols for reconstituting designer nucleosomes that contain specifically modified histones. The resulting nucleosomes are suitable for electromobility shift assays, chromatin remodeling assays, and other functional and structural studies.

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Year:  2012        PMID: 22183598      PMCID: PMC3749000          DOI: 10.1007/978-1-61779-477-3_15

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  13 in total

Review 1.  Identification and analysis of native nucleosomal histone acetyltransferase complexes.

Authors:  P A Grant; S L Berger; J L Workman
Journal:  Methods Mol Biol       Date:  1999

Review 2.  Analysis of nucleosome disruption by ATP-driven chromatin remodeling complexes.

Authors:  T Owen-Hughes; R T Utley; D J Steger; J M West; S John; J Côté; K M Havas; J L Workman
Journal:  Methods Mol Biol       Date:  1999

Review 3.  Translating the histone code.

Authors:  T Jenuwein; C D Allis
Journal:  Science       Date:  2001-08-10       Impact factor: 47.728

Review 4.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification.

Authors:  O Puig; F Caspary; G Rigaut; B Rutz; E Bouveret; E Bragado-Nilsson; M Wilm; B Séraphin
Journal:  Methods       Date:  2001-07       Impact factor: 3.608

5.  Reconstitution of nucleosome core particles from recombinant histones and DNA.

Authors:  Pamela N Dyer; Raji S Edayathumangalam; Cindy L White; Yunhe Bao; Srinivas Chakravarthy; Uma M Muthurajan; Karolin Luger
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

Review 6.  Epigenetics, histone H3 variants, and the inheritance of chromatin states.

Authors:  S Henikoff; E McKittrick; K Ahmad
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2004

Review 7.  Chromatin modifications and their function.

Authors:  Tony Kouzarides
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

Review 8.  The role of chromatin during transcription.

Authors:  Bing Li; Michael Carey; Jerry L Workman
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

9.  Histone H4-K16 acetylation controls chromatin structure and protein interactions.

Authors:  Michael Shogren-Knaak; Haruhiko Ishii; Jian-Min Sun; Michael J Pazin; James R Davie; Craig L Peterson
Journal:  Science       Date:  2006-02-10       Impact factor: 47.728

10.  A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation.

Authors:  Heinz Neumann; Susan M Hancock; Ruth Buning; Andrew Routh; Lynda Chapman; Joanna Somers; Tom Owen-Hughes; John van Noort; Daniela Rhodes; Jason W Chin
Journal:  Mol Cell       Date:  2009-10-09       Impact factor: 17.970

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  13 in total

1.  Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex.

Authors:  Chun Ruan; Haochen Cui; Chul-Hwan Lee; Sheng Li; Bing Li
Journal:  J Biol Chem       Date:  2016-01-08       Impact factor: 5.157

Review 2.  Touch, act and go: landing and operating on nucleosomes.

Authors:  Valentina Speranzini; Simona Pilotto; Titia K Sixma; Andrea Mattevi
Journal:  EMBO J       Date:  2016-01-19       Impact factor: 11.598

3.  Multivalent di-nucleosome recognition enables the Rpd3S histone deacetylase complex to tolerate decreased H3K36 methylation levels.

Authors:  Jae-Wan Huh; Jun Wu; Chul-Hwan Lee; Miyong Yun; Daniel Gilada; Chad A Brautigam; Bing Li
Journal:  EMBO J       Date:  2012-08-03       Impact factor: 11.598

4.  Preparation and analysis of positioned mononucleosomes.

Authors:  Olga I Kulaeva; Vasily M Studitsky
Journal:  Methods Mol Biol       Date:  2015

5.  Combinatorial Histone Readout by the Dual Plant Homeodomain (PHD) Fingers of Rco1 Mediates Rpd3S Chromatin Recruitment and the Maintenance of Transcriptional Fidelity.

Authors:  Stephen L McDaniel; Jennifer E Fligor; Chun Ruan; Haochen Cui; Joseph B Bridgers; Julia V DiFiore; Angela H Guo; Bing Li; Brian D Strahl
Journal:  J Biol Chem       Date:  2016-05-16       Impact factor: 5.157

6.  Nucleosome contact triggers conformational changes of Rpd3S driving high-affinity H3K36me nucleosome engagement.

Authors:  Chun Ruan; Chul-Hwan Lee; Haochen Cui; Sheng Li; Bing Li
Journal:  Cell Rep       Date:  2015-01-08       Impact factor: 9.423

Review 7.  Pioneer factors and their in vitro identification methods.

Authors:  Xinyang Yu; Michael J Buck
Journal:  Mol Genet Genomics       Date:  2020-04-15       Impact factor: 3.291

8.  Allosteric Activation Dictates PRC2 Activity Independent of Its Recruitment to Chromatin.

Authors:  Chul-Hwan Lee; Jia-Ray Yu; Sunil Kumar; Ying Jin; Gary LeRoy; Natarajan Bhanu; Syuzo Kaneko; Benjamin A Garcia; Andrew D Hamilton; Danny Reinberg
Journal:  Mol Cell       Date:  2018-04-19       Impact factor: 17.970

9.  Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire.

Authors:  Fu Huang; Ariel Paulson; Arnob Dutta; Swaminathan Venkatesh; Michaela Smolle; Susan M Abmayr; Jerry L Workman
Journal:  Genes Dev       Date:  2014-12-15       Impact factor: 11.361

10.  Capturing the Onset of PRC2-Mediated Repressive Domain Formation.

Authors:  Ozgur Oksuz; Varun Narendra; Chul-Hwan Lee; Nicolas Descostes; Gary LeRoy; Ramya Raviram; Lili Blumenberg; Kelly Karch; Pedro P Rocha; Benjamin A Garcia; Jane A Skok; Danny Reinberg
Journal:  Mol Cell       Date:  2018-06-21       Impact factor: 17.970

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