Literature DB >> 25827893

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

Kseniya S Kudryashova1, Oleg V Chertkov, Dmitry V Nikitin, Nikolai A Pestov, Olga I Kulaeva, Anastasija V Efremenko, Alexander S Solonin, Mikhail P Kirpichnikov, Vasily M Studitsky, Alexey V Feofanov.   

Abstract

Single positioned nucleosomes have been extensively employed as simple model experimental systems for analysis of various intranuclear processes. Here we describe an experimental system containing positioned mononucleosomes allowing transcription by various RNA polymerases. Each DNA template contains a pair of fluorescent labels (Cy3 and Cy5) allowing measuring relative distances between the neighboring coils of nucleosomal DNA using Forster resonance energy transfer (FRET). The single-particle FRET (spFRET) approach for analysis of DNA uncoiling from the histone octamer during transcription through chromatin is described in detail.

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Year:  2015        PMID： 25827893      PMCID： PMC4966549          DOI： 10.1007/978-1-4939-2474-5_23

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


  35 in total

1.  Preparation of nucleosome core particle from recombinant histones.

Authors:  K Luger; T J Rechsteiner; T J Richmond
Journal:  Methods Enzymol       Date:  1999       Impact factor: 1.600

2.  Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.

Authors:  A Thåström; P T Lowary; H R Widlund; H Cao; M Kubista; J Widom
Journal:  J Mol Biol       Date:  1999-04-30       Impact factor: 5.469

3.  Effects of DNA methylation on the structure of nucleosomes.

Authors:  Ju Yeon Lee; Tae-Hee Lee
Journal:  J Am Chem Soc       Date:  2011-12-15       Impact factor: 15.419

4.  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

5.  Preparation of defined mononucleosomes, dinucleosomes, and nucleosome arrays in vitro and analysis of transcription factor binding.

Authors:  Lisa Ann Cirillo; Kenneth S Zaret
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

6.  Approaches for studying nucleosome movement by ATP-dependent chromatin remodeling complexes.

Authors:  Swetansu K Hota; Blaine Bartholomew
Journal:  Methods Mol Biol       Date:  2012

7.  Histone Sin mutations promote nucleosome traversal and histone displacement by RNA polymerase II.

Authors:  Fu-Kai Hsieh; Michael Fisher; Andrea Ujvári; Vasily M Studitsky; Donal S Luse
Journal:  EMBO Rep       Date:  2010-08-13       Impact factor: 8.807

8.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

Review 9.  Effects of histone acetylation and CpG methylation on the structure of nucleosomes.

Authors:  Ju Yeon Lee; Tae-Hee Lee
Journal:  Biochim Biophys Acta       Date:  2012-05-22

10.  The ATP-dependent remodeler RSC transfers histone dimers and octamers through the rapid formation of an unstable encounter intermediate.

Authors:  Claire E Rowe; Geeta J Narlikar
Journal:  Biochemistry       Date:  2010-10-25       Impact factor: 3.162
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  9 in total

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

Authors:  Tatyana V Andreeva; Natalya V Maluchenko; Anastasiia L Sivkina; Oleg V Chertkov; Maria E Valieva; Elena Y Kotova; Mikhail P Kirpichnikov; Vasily M Studitsky; Alexey V Feofanov
Journal:  Microsc Microanal       Date:  2022-02       Impact factor: 4.099

2.  Time-resolved analysis of transcription through chromatin.

Authors:  Han-Wen Chang; Fu-Kai Hsieh; Smita S Patel; Vasily M Studitsky
Journal:  Methods       Date:  2019-01-29       Impact factor: 3.608

3.  Large-scale ATP-independent nucleosome unfolding by a histone chaperone.

Authors:  Maria E Valieva; Grigoriy A Armeev; Kseniya S Kudryashova; Nadezhda S Gerasimova; Alexey K Shaytan; Olga I Kulaeva; Laura L McCullough; Tim Formosa; Pavel G Georgiev; Mikhail P Kirpichnikov; Vasily M Studitsky; Alexey V Feofanov
Journal:  Nat Struct Mol Biol       Date:  2016-11-07       Impact factor: 18.361

4.  Unfolding of core nucleosomes by PARP-1 revealed by spFRET microscopy.

Authors:  Daniel C Sultanov; Nadezhda S Gerasimova; Kseniya S Kudryashova; Natalya V Maluchenko; Elena Y Kotova; Marie-France Langelier; John M Pascal; Mikhail P Kirpichnikov; Alexey V Feofanov; Vasily M Studitsky
Journal:  AIMS Genet       Date:  2017-01-05

5.  Electron microscopy analysis of ATP-independent nucleosome unfolding by FACT.

Authors:  Anastasiia L Sivkina; Maria G Karlova; Maria E Valieva; Laura L McCullough; Timothy Formosa; Alexey K Shaytan; Alexey V Feofanov; Mikhail P Kirpichnikov; Olga S Sokolova; Vasily M Studitsky
Journal:  Commun Biol       Date:  2022-01-10

6.  N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro.

Authors:  Han-Wen Chang; Alexey V Feofanov; Alexander V Lyubitelev; Grigory A Armeev; Elena Y Kotova; Fu-Kai Hsieh; Mikhail P Kirpichnikov; Alexey K Shaytan; Vasily M Studitsky
Journal:  Cells       Date:  2022-08-10       Impact factor: 7.666

7.  Hmo1 Protein Affects the Nucleosome Structure and Supports the Nucleosome Reorganization Activity of Yeast FACT.

Authors:  Daria K Malinina; Anastasiia L Sivkina; Anna N Korovina; Laura L McCullough; Tim Formosa; Mikhail P Kirpichnikov; Vasily M Studitsky; Alexey V Feofanov
Journal:  Cells       Date:  2022-09-20       Impact factor: 7.666

8.  Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy.

Authors:  Maria E Valieva; Nadezhda S Gerasimova; Kseniya S Kudryashova; Anastasia L Kozlova; Mikhail P Kirpichnikov; Qi Hu; Maria Victoria Botuyan; Georges Mer; Alexey V Feofanov; Vasily M Studitsky
Journal:  Cancers (Basel)       Date:  2017-01-06       Impact factor: 6.575

9.  Molecular Mechanisms of PARP-1 Inhibitor 7-Methylguanine.

Authors:  Dmitry Nilov; Natalya Maluchenko; Tatyana Kurgina; Sergey Pushkarev; Alexandra Lys; Mikhail Kutuzov; Nadezhda Gerasimova; Alexey Feofanov; Vytas Švedas; Olga Lavrik; Vasily M Studitsky
Journal:  Int J Mol Sci       Date:  2020-03-20       Impact factor: 5.923
  9 in total

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