Literature DB >> 22929776

A chemical approach to mapping nucleosomes at base pair resolution in yeast.

Kristin R Brogaard1, Liqun Xi, Ji-Ping Wang, Jonathan Widom.   

Abstract

Most eukaryotic DNA exists in DNA-protein complexes known as nucleosomes. The exact locations of nucleosomes along the genome play a critical role in chromosome functions and gene regulation. However, the current methods for nucleosome mapping do not provide the necessary accuracy to identify the precise nucleosome locations. Here we describe a new experimental approach that directly maps nucleosome center locations in vivo genome-wide at single base pair resolution.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID： 22929776      PMCID： PMC5101424          DOI： 10.1016/B978-0-12-391938-0.00014-8

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


  19 in total

1.  The structure of DNA in the nucleosome core.

Authors:  Timothy J Richmond; Curt A Davey
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

2.  Rapid spontaneous accessibility of nucleosomal DNA.

Authors:  Gu Li; Marcia Levitus; Carlos Bustamante; Jonathan Widom
Journal:  Nat Struct Mol Biol       Date:  2004-12-05       Impact factor: 15.369

3.  Effect of osmolytes as folding aids on creatine kinase refolding pathway.

Authors:  Wen-Bin Ou; Yong-Doo Park; Hai-Meng Zhou
Journal:  Int J Biochem Cell Biol       Date:  2002-02       Impact factor: 5.085

4.  The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere.

Authors:  Hope A Cole; Bruce H Howard; David J Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-18       Impact factor: 11.205

5.  High sequence specificity of micrococcal nuclease.

Authors:  C Dingwall; G P Lomonossoff; R A Laskey
Journal:  Nucleic Acids Res       Date:  1981-06-25       Impact factor: 16.971

6.  Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals.

Authors:  A Flaus; K Luger; S Tan; T J Richmond
Journal:  Proc Natl Acad Sci U S A       Date:  1996-02-20       Impact factor: 11.205

7.  A map of nucleosome positions in yeast at base-pair resolution.

Authors:  Kristin Brogaard; Liqun Xi; Ji-Ping Wang; Jonathan Widom
Journal:  Nature       Date:  2012-06-28       Impact factor: 49.962

8.  Occlusion of regulatory sequences by promoter nucleosomes in vivo.

Authors:  Changhui Mao; Christopher R Brown; Joachim Griesenbeck; Hinrich Boeger
Journal:  PLoS One       Date:  2011-03-03       Impact factor: 3.240

9.  Trapping DNA-protein binding reactions with neutral osmolytes for the analysis by gel mobility shift and self-cleavage assays.

Authors:  Nina Y Sidorova; Shakir Muradymov; Donald C Rau
Journal:  Nucleic Acids Res       Date:  2005-09-09       Impact factor: 16.971

10.  Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.

Authors:  Vladimir B Teif; Karsten Rippe
Journal:  Nucleic Acids Res       Date:  2009-07-22       Impact factor: 16.971
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  15 in total

Review 1.  Nucleosome positioning in yeasts: methods, maps, and mechanisms.

Authors:  Corinna Lieleg; Nils Krietenstein; Maria Walker; Philipp Korber
Journal:  Chromosoma       Date:  2014-12-23       Impact factor: 4.316

Review 2.  Functional roles of nucleosome stability and dynamics.

Authors:  Răzvan V Chereji; Alexandre V Morozov
Journal:  Brief Funct Genomics       Date:  2014-09-30       Impact factor: 4.241

3.  Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.

Authors:  Erinija Pranckeviciene; Sergey Hosid; Indiras Maziukas; Ilya Ioshikhes
Journal:  Int J Mol Sci       Date:  2022-04-28       Impact factor: 6.208

4.  Ubiquitous nucleosome crowding in the yeast genome.

Authors:  Răzvan V Chereji; Alexandre V Morozov
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-24       Impact factor: 11.205

5.  Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.

Authors:  Georgette Moyle-Heyrman; Tetiana Zaichuk; Liqun Xi; Quanwei Zhang; Olke C Uhlenbeck; Robert Holmgren; Jonathan Widom; Ji-Ping Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-25       Impact factor: 11.205

6.  Poly-dA:dT tracts form an in vivo nucleosomal turnstile.

Authors:  Carl G de Boer; Timothy R Hughes
Journal:  PLoS One       Date:  2014-10-29       Impact factor: 3.240

7.  Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.

Authors:  Narasimharao Nalabothula; Liqun Xi; Sucharita Bhattacharyya; Jonathan Widom; Ji-Ping Wang; John N Reeve; Thomas J Santangelo; Yvonne N Fondufe-Mittendorf
Journal:  BMC Genomics       Date:  2013-06-10       Impact factor: 3.969

8.  The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.

Authors:  Steven Henikoff; Srinivas Ramachandran; Kristina Krassovsky; Terri D Bryson; Christine A Codomo; Kristin Brogaard; Jonathan Widom; Ji-Ping Wang; Jorja G Henikoff
Journal:  Elife       Date:  2014-04-15       Impact factor: 8.140

9.  Asymmetric nucleosomes flank promoters in the budding yeast genome.

Authors:  Srinivas Ramachandran; Gabriel E Zentner; Steven Henikoff
Journal:  Genome Res       Date:  2014-12-09       Impact factor: 9.043

10.  Involvement of PARP1 in the regulation of alternative splicing.

Authors:  Elena Matveeva; John Maiorano; Qingyang Zhang; Abdallah M Eteleeb; Paolo Convertini; Jing Chen; Vittoria Infantino; Stefan Stamm; Jiping Wang; Eric C Rouchka; Yvonne N Fondufe-Mittendorf
Journal:  Cell Discov       Date:  2016-02-16       Impact factor: 10.849
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