Literature DB >> 18339538

Chromatin state maps: new technologies, new insights.

Eric M Mendenhall1, Bradley E Bernstein.   

Abstract

Recent years have seen unprecedented characterization of mammalian chromatin thanks to advances in chromatin assays, antibody development, and genomics. Genome-wide maps of chromatin state can now be readily acquired using microarrays or next-generation sequencing technologies. These datasets reveal local and long-range chromatin patterns that offer insight into the locations and functions of underlying regulatory elements and genes. These patterns are dynamic across developmental stages and lineages. Global studies of chromatin in embryonic stem cells have led to intriguing hypotheses regarding Polycomb/trithorax and RNA polymerase roles in 'poising' transcription. Chromatin state maps thus provide a rich resource for understanding chromatin at a 'systems level', and a starting point for mechanistic studies aimed at defining epigenetic controls that underlie development.

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Year:  2008        PMID: 18339538      PMCID: PMC2486450          DOI: 10.1016/j.gde.2008.01.010

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  49 in total

1.  Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing.

Authors:  Robert J Sims; Scott Millhouse; Chi-Fu Chen; Brian A Lewis; Hediye Erdjument-Bromage; Paul Tempst; James L Manley; Danny Reinberg
Journal:  Mol Cell       Date:  2007-11-30       Impact factor: 17.970

Review 2.  Histone lysine demethylases: emerging roles in development, physiology and disease.

Authors:  Yang Shi
Journal:  Nat Rev Genet       Date:  2007-11       Impact factor: 53.242

3.  A chromatin landmark and transcription initiation at most promoters in human cells.

Authors:  Matthew G Guenther; Stuart S Levine; Laurie A Boyer; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2007-07-13       Impact factor: 41.582

4.  Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.

Authors:  Xiao Dong Zhao; Xu Han; Joon Lin Chew; Jun Liu; Kuo Ping Chiu; Andre Choo; Yuriy L Orlov; Wing-Kin Sung; Atif Shahab; Vladimir A Kuznetsov; Guillaume Bourque; Steve Oh; Yijun Ruan; Huck-Hui Ng; Chia-Lin Wei
Journal:  Cell Stem Cell       Date:  2007-09-13       Impact factor: 24.633

5.  Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells.

Authors:  Guangjin Pan; Shulan Tian; Jeff Nie; Chuhu Yang; Victor Ruotti; Hairong Wei; Gudrun A Jonsdottir; Ron Stewart; James A Thomson
Journal:  Cell Stem Cell       Date:  2007-09-13       Impact factor: 24.633

6.  Bmi-1 is required for maintenance of adult self-renewing haematopoietic stem cells.

Authors:  In-kyung Park; Dalong Qian; Mark Kiel; Michael W Becker; Michael Pihalja; Irving L Weissman; Sean J Morrison; Michael F Clarke
Journal:  Nature       Date:  2003-04-20       Impact factor: 49.962

7.  RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.

Authors:  Julia Zeitlinger; Alexander Stark; Manolis Kellis; Joung-Woo Hong; Sergei Nechaev; Karen Adelman; Michael Levine; Richard A Young
Journal:  Nat Genet       Date:  2007-11-11       Impact factor: 38.330

8.  Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells.

Authors:  Julie K Stock; Sara Giadrossi; Miguel Casanova; Emily Brookes; Miguel Vidal; Haruhiko Koseki; Neil Brockdorff; Amanda G Fisher; Ana Pombo
Journal:  Nat Cell Biol       Date:  2007-11-25       Impact factor: 28.824

Review 9.  Histone deacetylases and cancer.

Authors:  M A Glozak; E Seto
Journal:  Oncogene       Date:  2007-08-13       Impact factor: 9.867

10.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:  Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal:  Nature       Date:  2007-07-01       Impact factor: 49.962

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  36 in total

1.  Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays.

Authors:  Ina Bock; Arunkumar Dhayalan; Srikanth Kudithipudi; Ole Brandt; Philipp Rathert; Albert Jeltsch
Journal:  Epigenetics       Date:  2011-02-01       Impact factor: 4.528

2.  Comprehensive profiling reveals mechanisms of SOX2-mediated cell fate specification in human ESCs and NPCs.

Authors:  Chenlin Zhou; Xiaoqin Yang; Yiyang Sun; Hongyao Yu; Yong Zhang; Ying Jin
Journal:  Cell Res       Date:  2016-01-26       Impact factor: 25.617

Review 3.  Chromatin signatures of active enhancers.

Authors:  Salvatore Spicuglia; Laurent Vanhille
Journal:  Nucleus       Date:  2012-03-01       Impact factor: 4.197

4.  A histone demethylase is necessary for regeneration in zebrafish.

Authors:  Scott Stewart; Zhi-Yang Tsun; Juan Carlos Izpisua Belmonte
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-06       Impact factor: 11.205

5.  H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Authors:  Aleksandra Pekowska; Touati Benoukraf; Joaquin Zacarias-Cabeza; Mohamed Belhocine; Frederic Koch; Hélène Holota; Jean Imbert; Jean-Christophe Andrau; Pierre Ferrier; Salvatore Spicuglia
Journal:  EMBO J       Date:  2011-08-16       Impact factor: 11.598

Review 6.  Mechanisms of polycomb gene silencing: knowns and unknowns.

Authors:  Jeffrey A Simon; Robert E Kingston
Journal:  Nat Rev Mol Cell Biol       Date:  2009-09-09       Impact factor: 94.444

7.  How has the study of the human placenta aided our understanding of partially methylated genes?

Authors:  Diane I Schroeder; Janine M LaSalle
Journal:  Epigenomics       Date:  2013-12       Impact factor: 4.778

8.  H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment.

Authors:  Menno P Creyghton; Styliani Markoulaki; Stuart S Levine; Jacob Hanna; Michael A Lodato; Ky Sha; Richard A Young; Rudolf Jaenisch; Laurie A Boyer
Journal:  Cell       Date:  2008-11-06       Impact factor: 41.582

9.  Additional sex combs-like 1 belongs to the enhancer of trithorax and polycomb group and genetically interacts with Cbx2 in mice.

Authors:  C L Fisher; I Lee; S Bloyer; S Bozza; J Chevalier; A Dahl; C Bodner; C D Helgason; J L Hess; R K Humphries; H W Brock
Journal:  Dev Biol       Date:  2009-10-13       Impact factor: 3.582

10.  Functional enhancers at the gene-poor 8q24 cancer-linked locus.

Authors:  Li Jia; Gilad Landan; Mark Pomerantz; Rami Jaschek; Paula Herman; David Reich; Chunli Yan; Omar Khalid; Phil Kantoff; William Oh; J Robert Manak; Benjamin P Berman; Brian E Henderson; Baruch Frenkel; Christopher A Haiman; Matthew Freedman; Amos Tanay; Gerhard A Coetzee
Journal:  PLoS Genet       Date:  2009-08-14       Impact factor: 5.917

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