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Literature DB >> 22910212

Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II.

Daria A Gaykalova¹, Olga I Kulaeva, Nikolai A Pestov, Fu-Kai Hsieh, Vasily M Studitsky.

Abstract

The vital process of transcription by RNA polymerase II (Pol II) occurs in chromatin environment in eukaryotic cells; in fact, moderately transcribed genes retain nucleosomal structure. Recent studies suggest that chromatin structure presents a strong barrier for transcribing Pol II in vitro, and that DNA-histone interactions are only partially and transiently disrupted during transcript elongation on moderately active genes. Furthermore, elongating Pol II complex is one of the major targets during gene regulation. Below, we describe a highly purified, defined experimental system that recapitulates many important properties of transcribed chromatin in vitro and allows detailed analysis of the underlying mechanisms.

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Year: 2012 PMID： 22910212 PMCID： PMC3926419 DOI： 10.1016/B978-0-12-391940-3.00013-5

Source DB: PubMed Journal: Methods Enzymol ISSN： 0076-6879 Impact factor: 1.600

52 in total

Review 1. Preparation and analysis of positioned nucleosomes.

Authors: V M Studitsky
Journal: Methods Mol Biol Date: 1999

2. Role of C-terminal domain phosphorylation in RNA polymerase II transcription through the nucleosome.

Authors: Y V Liu; D J Clark; V Tchernajenko; M E Dahmus; V M Studitsky
Journal: Biopolymers Date: 2003-04 Impact factor: 2.505

3. Assay of the fate of the nucleosome during transcription by RNA polymerase II.

Authors: W Walter; M L Kireeva; V Tchernajenko; M Kashlev; V M Studitsky
Journal: Methods Enzymol Date: 2003 Impact factor: 1.600

4. FACT facilitates transcription-dependent nucleosome alteration.

Authors: Rimma Belotserkovskaya; Sangtaek Oh; Vladimir A Bondarenko; George Orphanides; Vasily M Studitsky; Danny Reinberg
Journal: Science Date: 2003-08-22 Impact factor: 47.728

5. Transcription through the nucleosome by mRNA-producing RNA polymerases.

Authors: W Walter; M Kashlev; V M Studitsky
Journal: Methods Enzymol Date: 2004 Impact factor: 1.600

6. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo.

Authors: Arnold Kristjuhan; Jesper Q Svejstrup
Journal: EMBO J Date: 2004-09-30 Impact factor: 11.598

7. Mechanism of histone survival during transcription by RNA polymerase II.

Authors: Olga I Kulaeva; Vasily M Studitsky
Journal: Transcription Date: 2010 Sep-Oct

8. Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions.

Authors: R L Dedrick; M J Chamberlin
Journal: Biochemistry Date: 1985-04-23 Impact factor: 3.162

9. Assembly of RNA polymerase II preinitiation complexes before assembly of nucleosomes allows efficient initiation of transcription on nucleosomal templates.

Authors: J A Knezetic; G A Jacob; D S Luse
Journal: Mol Cell Biol Date: 1988-08 Impact factor: 4.272

8. A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity.

Authors: Cristina Voss; Brita Schmitt; Susanne Werner-Simon; Christian Lutz; Werner Simon; Jan Anderl
Journal: BMC Mol Biol Date: 2014-04-03 Impact factor: 2.946

8 in total

Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II.

Review 1. Preparation and analysis of positioned nucleosomes.

2. Role of C-terminal domain phosphorylation in RNA polymerase II transcription through the nucleosome.

3. Assay of the fate of the nucleosome during transcription by RNA polymerase II.

4. FACT facilitates transcription-dependent nucleosome alteration.

5. Transcription through the nucleosome by mRNA-producing RNA polymerases.

6. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo.

7. Mechanism of histone survival during transcription by RNA polymerase II.

8. Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions.

9. Assembly of RNA polymerase II preinitiation complexes before assembly of nucleosomes allows efficient initiation of transcription on nucleosomal templates.

10. Bacterial polymerase and yeast polymerase II use similar mechanisms for transcription through nucleosomes.

1. Experimental analysis of hFACT action during Pol II transcription in vitro.

2. Preparation and analysis of positioned mononucleosomes.

3. Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET.

4. Human PARP1 Facilitates Transcription through a Nucleosome and Histone Displacement by Pol II In Vitro.

5. Na⁺ and K⁺ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins.

6. Time-resolved analysis of transcription through chromatin.

7. Mechanism of RNA polymerase II stalling by DNA alkylation.

8. A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity.