Literature DB >> 24679523

Looping back to leap forward: transcription enters a new era.

Michael Levine1, Claudia Cattoglio2, Robert Tjian3.   

Abstract

Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
Copyright © 2014 Elsevier Inc. All rights reserved.

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Year:  2014        PMID： 24679523      PMCID： PMC4059561          DOI： 10.1016/j.cell.2014.02.009

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  137 in total

1.  Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

Authors:  A L Gnatt; P Cramer; J Fu; D A Bushnell; R D Kornberg
Journal:  Science       Date:  2001-04-19       Impact factor: 47.728

2.  Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.

Authors:  Michael D Shapiro; Melissa E Marks; Catherine L Peichel; Benjamin K Blackman; Kirsten S Nereng; Bjarni Jónsson; Dolph Schluter; David M Kingsley
Journal:  Nature       Date:  2004-04-15       Impact factor: 49.962

Review 3.  Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

4.  Structures of three distinct activator-TFIID complexes.

Authors:  Wei-Li Liu; Robert A Coleman; Elizabeth Ma; Patricia Grob; Joyce L Yang; Yixi Zhang; Gina Dailey; Eva Nogales; Robert Tjian
Journal:  Genes Dev       Date:  2009-07-01       Impact factor: 11.361

Review 5.  Nuclear RNA polymerases: role of general initiation factors and cofactors in eukaryotic transcription.

Authors:  R G Roeder
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

6.  Control of embryonic stem cell lineage commitment by core promoter factor, TAF3.

Authors:  Zhe Liu; Devin R Scannell; Michael B Eisen; Robert Tjian
Journal:  Cell       Date:  2011-09-02       Impact factor: 41.582

7.  Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes.

Authors:  Juan Manuel Caravaca; Greg Donahue; Justin S Becker; Ximiao He; Charles Vinson; Kenneth S Zaret
Journal:  Genes Dev       Date:  2013-01-25       Impact factor: 11.361

8.  Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription.

Authors:  Takanori Amano; Tomoko Sagai; Hideyuki Tanabe; Yoichi Mizushina; Hiromi Nakazawa; Toshihiko Shiroishi
Journal:  Dev Cell       Date:  2008-12-18       Impact factor: 12.270

Review 9.  Revisiting the central dogma one molecule at a time.

Authors:  Carlos Bustamante; Wei Cheng; Yara X Mejia; Yara X Meija
Journal:  Cell       Date:  2011-02-18       Impact factor: 41.582

10.  The formation and maintenance of the definitive endoderm lineage in the mouse: involvement of HNF3/forkhead proteins.

Authors:  S L Ang; A Wierda; D Wong; K A Stevens; S Cascio; J Rossant; K S Zaret
Journal:  Development       Date:  1993-12       Impact factor: 6.868
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  223 in total

1.  Mutations in the linker domain affect phospho-STAT3 function and suggest targets for interrupting STAT3 activity.

Authors:  Claudia Mertens; Bhagwattie Haripal; Sebastian Klinge; James E Darnell
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-09       Impact factor: 11.205

2.  CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Authors:  Ya Guo; Quan Xu; Daniele Canzio; Jia Shou; Jinhuan Li; David U Gorkin; Inkyung Jung; Haiyang Wu; Yanan Zhai; Yuanxiao Tang; Yichao Lu; Yonghu Wu; Zhilian Jia; Wei Li; Michael Q Zhang; Bing Ren; Adrian R Krainer; Tom Maniatis; Qiang Wu
Journal:  Cell       Date:  2015-08-13       Impact factor: 41.582

Review 3.  Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.

Authors:  Hyun-Jin Yang; Rinki Ratnapriya; Tiziana Cogliati; Jung-Woong Kim; Anand Swaroop
Journal:  Prog Retin Eye Res       Date:  2015-02-07       Impact factor: 21.198

4.  Mutant p53 regulates enhancer-associated H3K4 monomethylation through interactions with the methyltransferase MLL4.

Authors:  Homa Rahnamoun; Juyeong Hong; Zhengxi Sun; Jihoon Lee; Hanbin Lu; Shannon M Lauberth
Journal:  J Biol Chem       Date:  2018-06-28       Impact factor: 5.157

Review 5.  MLL3/MLL4/COMPASS Family on Epigenetic Regulation of Enhancer Function and Cancer.

Authors:  Christie C Sze; Ali Shilatifard
Journal:  Cold Spring Harb Perspect Med       Date:  2016-11-01       Impact factor: 6.915

6.  The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.

Authors:  Makiko Iwafuchi-Doi; Greg Donahue; Akshay Kakumanu; Jason A Watts; Shaun Mahony; B Franklin Pugh; Dolim Lee; Klaus H Kaestner; Kenneth S Zaret
Journal:  Mol Cell       Date:  2016-04-07       Impact factor: 17.970

7.  SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease.

Authors:  Yunmin Li; Tatsuo Kido; Maria M Garcia-Barcelo; Paul K H Tam; Z Laura Tabatabai; Yun-Fai Chris Lau
Journal:  Hum Mol Genet       Date:  2014-09-28       Impact factor: 6.150

Review 8.  What history tells us XXXV. Enhancers: their existence and characteristics have raised puzzling issues since their discovery.

Authors:  Michel Morange
Journal:  J Biosci       Date:  2014-12       Impact factor: 1.826

Review 9.  Elucidating the mechanisms of transcription regulation during heart development by next-generation sequencing.

Authors:  Keisuke Nimura; Yasufumi Kaneda
Journal:  J Hum Genet       Date:  2015-07-23       Impact factor: 3.172

Review 10.  Signaling and Gene Regulatory Networks in Mammalian Lens Development.

Authors:  Ales Cvekl; Xin Zhang
Journal:  Trends Genet       Date:  2017-08-31       Impact factor: 11.639
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