Literature DB >> 19378187

Analysis of distant communication on defined chromatin templates in vitro.

Yury S Polikanov1, Vasily M Studitsky.   

Abstract

Regulation of many biological processes in eukaryotes involves distant communication between the regulatory DNA sequences (e.g., enhancers) and their targets over the DNA regions organized in chromatin. However previously developed methods for analysis of communication in chromatin in vitro are artifact-prone and/or do not allow analysis of communication on physiologically relevant, saturated arrays of nucleosomes. Here we describe a method for quantitative analysis of the rate of distant communication in cis on saturated arrays of nucleosomes capable of forming the 30-nm chromatin fibers in vitro.

Entities:  

Mesh：

Substances：

Year:  2009        PMID： 19378187      PMCID： PMC5100816          DOI： 10.1007/978-1-60327-015-1_33

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


  47 in total

1.  DNA supercoiling allows enhancer action over a large distance.

Authors:  Y Liu; V Bondarenko; A Ninfa; V M Studitsky
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-11       Impact factor: 11.205

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

Review 3.  Chromatin remodelling and the interaction between enhancers and promoters in the beta-globin locus.

Authors:  Ann Dean
Journal:  Brief Funct Genomic Proteomic       Date:  2004-02

Review 4.  Biochemical analysis of enhancer-promoter communication in chromatin.

Authors:  Yury S Polikanov; Mikhail A Rubtsov; Vasily M Studitsky
Journal:  Methods       Date:  2007-03       Impact factor: 3.608

5.  Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Authors:  Yury S Polikanov; Vladimir A Bondarenko; Vladimir Tchernaenko; Yong I Jiang; Leonard C Lutter; Alexander Vologodskii; Vasily M Studitsky
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

6.  Rationally designed insulator-like elements can block enhancer action in vitro.

Authors:  Vladimir A Bondarenko; Yong I Jiang; Vasily M Studitsky
Journal:  EMBO J       Date:  2003-09-15       Impact factor: 11.598

7.  DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.

Authors:  W Su; S Porter; S Kustu; H Echols
Journal:  Proc Natl Acad Sci U S A       Date:  1990-07       Impact factor: 11.205

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

9.  DNA flexibility studied by covalent closure of short fragments into circles.

Authors:  D Shore; J Langowski; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-08       Impact factor: 11.205

10.  Long-range chromatin regulatory interactions in vivo.

Authors:  David Carter; Lyubomira Chakalova; Cameron S Osborne; Yan-feng Dai; Peter Fraser
Journal:  Nat Genet       Date:  2002-11-11       Impact factor: 38.330
View more
  7 in total

1.  Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators.

Authors:  Swagatam Mukhopadhyay; Paul Schedl; Vasily M Studitsky; Anirvan M Sengupta
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-28       Impact factor: 11.205

2.  Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.

Authors:  Olga I Kulaeva; Guohui Zheng; Yury S Polikanov; Andrew V Colasanti; Nicolas Clauvelin; Swagatam Mukhopadhyay; Anirvan M Sengupta; Vasily M Studitsky; Wilma K Olson
Journal:  J Biol Chem       Date:  2012-04-19       Impact factor: 5.157

3.  [Opposite Effects of Histone H1 and HMGN5 Protein on Distant Interactions in Chromatin].

Authors:  E V Nizovtseva; Y S Polikanov; O I Kulaeva; N Clauvelin; Y V Postnikov; W K Olson; V M Studitsky
Journal:  Mol Biol (Mosk)       Date:  2019 Nov-Dec

Review 4.  Towards quantitative analysis of gene regulation by enhancers.

Authors:  Ekaterina V Nizovtseva; Stefjord Todolli; Wilma K Olson; Vasily M Studitsky
Journal:  Epigenomics       Date:  2017-08-11       Impact factor: 4.778

5.  Insights into Gene Expression and Packaging from Computer Simulations.

Authors:  Wilma K Olson; Nicolas Clauvelin; Andrew V Colasanti; Gautam Singh; Guohui Zheng
Journal:  Biophys Rev       Date:  2012-09-01

6.  The anti-cancer drugs curaxins target spatial genome organization.

Authors:  Omar L Kantidze; Artem V Luzhin; Ekaterina V Nizovtseva; Alfiya Safina; Maria E Valieva; Arkadiy K Golov; Artem K Velichko; Alexander V Lyubitelev; Alexey V Feofanov; Katerina V Gurova; Vasily M Studitsky; Sergey V Razin
Journal:  Nat Commun       Date:  2019-03-29       Impact factor: 14.919

7.  Nucleosome-free DNA regions differentially affect distant communication in chromatin.

Authors:  Ekaterina V Nizovtseva; Nicolas Clauvelin; Stefjord Todolli; Yury S Polikanov; Olga I Kulaeva; Scott Wengrzynek; Wilma K Olson; Vasily M Studitsky
Journal:  Nucleic Acids Res       Date:  2017-04-07       Impact factor: 16.971
  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.