Literature DB >> 21116306

Charting histone modifications and the functional organization of mammalian genomes.

Vicky W Zhou1, Alon Goren, Bradley E Bernstein.   

Abstract

A succession of technological advances over the past decade have enabled researchers to chart maps of histone modifications and related chromatin structures with increasing accuracy, comprehensiveness and throughput. The resulting data sets highlight the interplay between chromatin and genome function, dynamic variations in chromatin structure across cellular conditions, and emerging roles for large-scale domains and higher-ordered chromatin organization. Here we review a selection of recent studies that have probed histone modifications and successive layers of chromatin structure in mammalian genomes, the patterns that have been identified and future directions for research.

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Year:  2010        PMID: 21116306     DOI: 10.1038/nrg2905

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  114 in total

1.  Gene regulation through nuclear organization.

Authors:  Tom Sexton; Heiko Schober; Peter Fraser; Susan M Gasser
Journal:  Nat Struct Mol Biol       Date:  2007-11-05       Impact factor: 15.369

2.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors:  Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal:  Nat Genet       Date:  2007-02-04       Impact factor: 38.330

3.  CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex.

Authors:  Jeong-Heon Lee; David G Skalnik
Journal:  J Biol Chem       Date:  2005-10-26       Impact factor: 5.157

4.  Control of inducible gene expression by signal-dependent transcriptional elongation.

Authors:  Diana C Hargreaves; Tiffany Horng; Ruslan Medzhitov
Journal:  Cell       Date:  2009-07-10       Impact factor: 41.582

5.  Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Authors:  Hong Ji; Lauren I R Ehrlich; Jun Seita; Peter Murakami; Akiko Doi; Paul Lindau; Hwajin Lee; Martin J Aryee; Rafael A Irizarry; Kitai Kim; Derrick J Rossi; Matthew A Inlay; Thomas Serwold; Holger Karsunky; Lena Ho; George Q Daley; Irving L Weissman; Andrew P Feinberg
Journal:  Nature       Date:  2010-08-15       Impact factor: 49.962

6.  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

7.  Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas.

Authors:  Neerja Karnani; Christopher Taylor; Ankit Malhotra; Anindya Dutta
Journal:  Genome Res       Date:  2007-06       Impact factor: 9.043

8.  Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.

Authors:  Jamy C Peng; Anton Valouev; Tomek Swigut; Junmei Zhang; Yingming Zhao; Arend Sidow; Joanna Wysocka
Journal:  Cell       Date:  2009-12-24       Impact factor: 41.582

9.  AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2.

Authors:  Hana Kim; Keunsoo Kang; Joomyeong Kim
Journal:  Nucleic Acids Res       Date:  2009-03-17       Impact factor: 16.971

10.  Recruitment to the nuclear periphery can alter expression of genes in human cells.

Authors:  Lee E Finlan; Duncan Sproul; Inga Thomson; Shelagh Boyle; Elizabeth Kerr; Paul Perry; Bauke Ylstra; Jonathan R Chubb; Wendy A Bickmore
Journal:  PLoS Genet       Date:  2008-03-21       Impact factor: 5.917

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  566 in total

Review 1.  The roles and regulation of Polycomb complexes in neural development.

Authors:  Matthew Corley; Kristen L Kroll
Journal:  Cell Tissue Res       Date:  2014-11-01       Impact factor: 5.249

2.  A Review of Mitochondrial-derived Fatty Acids in Epigenetic Regulation of Obesity and Type 2 Diabetes.

Authors:  Erin M Taylor; Aarin D Jones; Tara M Henagan
Journal:  J Nutrit Health Food Sci       Date:  2014-08-07

3.  Operating on chromatin, a colorful language where context matters.

Authors:  Kathryn E Gardner; C David Allis; Brian D Strahl
Journal:  J Mol Biol       Date:  2011-01-25       Impact factor: 5.469

Review 4.  Epigenetics and the environment: emerging patterns and implications.

Authors:  Robert Feil; Mario F Fraga
Journal:  Nat Rev Genet       Date:  2012-01-04       Impact factor: 53.242

5.  Epigenetic interplay between mouse endogenous retroviruses and host genes.

Authors:  Rita Rebollo; Katharine Miceli-Royer; Ying Zhang; Sharareh Farivar; Liane Gagnier; Dixie L Mager
Journal:  Genome Biol       Date:  2012-10-03       Impact factor: 13.583

6.  The signal transducers STAT5 and STAT3 control expression of Id2 and E2-2 during dendritic cell development.

Authors:  Haiyan S Li; Cliff Y Yang; Kalyan C Nallaparaju; Huiyuan Zhang; Yong-Jun Liu; Ananda W Goldrath; Stephanie S Watowich
Journal:  Blood       Date:  2012-10-01       Impact factor: 22.113

7.  An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.

Authors:  Birgit Knoechel; Justine E Roderick; Kaylyn E Williamson; Jiang Zhu; Jens G Lohr; Matthew J Cotton; Shawn M Gillespie; Daniel Fernandez; Manching Ku; Hongfang Wang; Federica Piccioni; Serena J Silver; Mohit Jain; Daniel Pearson; Michael J Kluk; Christopher J Ott; Leonard D Shultz; Michael A Brehm; Dale L Greiner; Alejandro Gutierrez; Kimberly Stegmaier; Andrew L Kung; David E Root; James E Bradner; Jon C Aster; Michelle A Kelliher; Bradley E Bernstein
Journal:  Nat Genet       Date:  2014-03-02       Impact factor: 38.330

8.  SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.

Authors:  Ying-Chung Lin; Wei Li; Ying-Hsuan Sun; Sapna Kumari; Hairong Wei; Quanzi Li; Sermsawat Tunlaya-Anukit; Ronald R Sederoff; Vincent L Chiang
Journal:  Plant Cell       Date:  2013-11-26       Impact factor: 11.277

Review 9.  Using chromatin marks to interpret and localize genetic associations to complex human traits and diseases.

Authors:  Gosia Trynka; Soumya Raychaudhuri
Journal:  Curr Opin Genet Dev       Date:  2013-11-25       Impact factor: 5.578

10.  H3F3A K27M mutations in thalamic gliomas from young adult patients.

Authors:  Koki Aihara; Akitake Mukasa; Kengo Gotoh; Kuniaki Saito; Genta Nagae; Shingo Tsuji; Kenji Tatsuno; Shogo Yamamoto; Shunsaku Takayanagi; Yoshitaka Narita; Soichiro Shibui; Hiroyuki Aburatani; Nobuhito Saito
Journal:  Neuro Oncol       Date:  2013-11-26       Impact factor: 12.300

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