Literature DB >> 19208466

Poly(dA:dT) tracts: major determinants of nucleosome organization.

Eran Segal1, Jonathan Widom.   

Abstract

Homopolymeric stretches of deoxyadenosine nucleotides (A's) on one strand of double-stranded DNA, referred to as poly(dA:dT) tracts or A-tracts, are overabundant in eukaryotic genomes. They have unusual structural, dynamic, and mechanical properties, and may resist sharp bending. Such unusual material properties, together with their overabundance in eukaryotes, raised the possibility that poly(dA:dT) tracts might function in eukaryotes to influence the organization of nucleosomes at many genomic regions. Recent genome-wide studies strongly confirm these ideas and suggest that these tracts play major roles in chromatin organization and genome function. Here we review what is known about poly(dA:dT) tracts and how they work.

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Year:  2009        PMID: 19208466      PMCID: PMC2673466          DOI: 10.1016/j.sbi.2009.01.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  58 in total

1.  Poly(dA).poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter.

Authors:  R Losa; S Omari; F Thoma
Journal:  Nucleic Acids Res       Date:  1990-06-25       Impact factor: 16.971

2.  Cooperativity in A-tract structure and bending properties of composite TnAn blocks.

Authors:  T E Haran; D M Crothers
Journal:  Biochemistry       Date:  1989-04-04       Impact factor: 3.162

3.  The structure of an oligo(dA).oligo(dT) tract and its biological implications.

Authors:  H C Nelson; J T Finch; B F Luisi; A Klug
Journal:  Nature       Date:  1987 Nov 19-25       Impact factor: 49.962

4.  Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism.

Authors:  R D Kornberg; L Stryer
Journal:  Nucleic Acids Res       Date:  1988-07-25       Impact factor: 16.971

5.  Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature.

Authors:  J L Leroy; E Charretier; M Kochoyan; M Guéron
Journal:  Biochemistry       Date:  1988-12-13       Impact factor: 3.162

6.  Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase.

Authors:  W Chen; S Tabor; K Struhl
Journal:  Cell       Date:  1987-09-25       Impact factor: 41.582

7.  Constitutive and inducible Saccharomyces cerevisiae promoters: evidence for two distinct molecular mechanisms.

Authors:  K Struhl
Journal:  Mol Cell Biol       Date:  1986-11       Impact factor: 4.272

8.  Activation of yeast RNA polymerase II transcription by a thymidine-rich upstream element in vitro.

Authors:  N F Lue; A R Buchman; R D Kornberg
Journal:  Proc Natl Acad Sci U S A       Date:  1989-01       Impact factor: 11.205

9.  A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts.

Authors:  E Winter; A Varshavsky
Journal:  EMBO J       Date:  1989-06       Impact factor: 11.598

10.  Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT).

Authors:  A Prunell
Journal:  EMBO J       Date:  1982       Impact factor: 11.598

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  209 in total

1.  Modeling DNA-bending in the nucleosome: role of AA periodicity.

Authors:  Tatiana R Prytkova; Xiao Zhu; Jonathan Widom; George C Schatz
Journal:  J Phys Chem B       Date:  2011-06-16       Impact factor: 2.991

2.  A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

Authors:  Judith B Zaugg; Nicholas M Luscombe
Journal:  Genome Res       Date:  2011-09-19       Impact factor: 9.043

3.  Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.

Authors:  Danny Zeevi; Eilon Sharon; Maya Lotan-Pompan; Yaniv Lubling; Zohar Shipony; Tali Raveh-Sadka; Leeat Keren; Michal Levo; Adina Weinberger; Eran Segal
Journal:  Genome Res       Date:  2011-10-18       Impact factor: 9.043

4.  Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast.

Authors:  Tali Raveh-Sadka; Michal Levo; Uri Shabi; Boaz Shany; Leeat Keren; Maya Lotan-Pompan; Danny Zeevi; Eilon Sharon; Adina Weinberger; Eran Segal
Journal:  Nat Genet       Date:  2012-05-27       Impact factor: 38.330

Review 5.  Regulation of DNA replication by chromatin structures: accessibility and recruitment.

Authors:  Makoto T Hayashi; Hisao Masukata
Journal:  Chromosoma       Date:  2010-08-03       Impact factor: 4.316

6.  Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.

Authors:  Evgenia N Nikolova; Gavin D Bascom; Ioan Andricioaei; Hashim M Al-Hashimi
Journal:  Biochemistry       Date:  2012-10-18       Impact factor: 3.162

7.  DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis.

Authors:  Shay Shilo; Cathy Melamed-Bessudo; Yanniv Dorone; Naama Barkai; Avraham A Levy
Journal:  Plant Cell       Date:  2015-09-17       Impact factor: 11.277

8.  Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships.

Authors:  Christopher M Jakobson; Daniel F Jarosz
Journal:  Cell Syst       Date:  2019-05-01       Impact factor: 10.304

9.  Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes.

Authors:  Alberto Marin-Gonzalez; Cesar L Pastrana; Rebeca Bocanegra; Alejandro Martín-González; J G Vilhena; Rubén Pérez; Borja Ibarra; Clara Aicart-Ramos; Fernando Moreno-Herrero
Journal:  Nucleic Acids Res       Date:  2020-05-21       Impact factor: 16.971

10.  The cis-regulatory effect of an Alzheimer's disease-associated poly-T locus on expression of TOMM40 and apolipoprotein E genes.

Authors:  Colton Linnertz; Lauren Anderson; William Gottschalk; Donna Crenshaw; Michael W Lutz; Jawara Allen; Sunita Saith; Mirta Mihovilovic; James R Burke; Kathleen A Welsh-Bohmer; Allen D Roses; Ornit Chiba-Falek
Journal:  Alzheimers Dement       Date:  2014-01-15       Impact factor: 21.566

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