Literature DB >> 19854636

Finding distal regulatory elements in the human genome.

Nathaniel D Heintzman1, Bing Ren.   

Abstract

Transcriptional regulation of human genes depends not only on promoters and nearby cis-regulatory elements, but also on distal regulatory elements such as enhancers, insulators, locus control regions, and silencing elements, which are often located far away from the genes they control. Our knowledge of human distal regulatory elements is very limited, but the last several years have seen rapid progress in the development of strategies to identify these long-range regulatory sequences throughout the human genome. Here, we review these advances, focusing on two important classes of distal regulatory sequences-enhancers and insulators.

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Year:  2009        PMID： 19854636      PMCID： PMC3321269          DOI： 10.1016/j.gde.2009.09.006

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


  61 in total

Review 1.  The coregulator exchange in transcriptional functions of nuclear receptors.

Authors:  C K Glass; M G Rosenfeld
Journal:  Genes Dev       Date:  2000-01-15       Impact factor: 11.361

2.  The language of covalent histone modifications.

Authors:  B D Strahl; C D Allis
Journal:  Nature       Date:  2000-01-06       Impact factor: 49.962

Review 3.  Insulators and boundaries: versatile regulatory elements in the eukaryotic genome.

Authors:  A C Bell; A G West; G Felsenfeld
Journal:  Science       Date:  2001-01-19       Impact factor: 47.728

Review 4.  Transcription of eukaryotic protein-coding genes.

Authors:  T I Lee; R A Young
Journal:  Annu Rev Genet       Date:  2000       Impact factor: 16.830

Review 5.  Orchestrated response: a symphony of transcription factors for gene control.

Authors:  B Lemon; R Tjian
Journal:  Genes Dev       Date:  2000-10-15       Impact factor: 11.361

6.  CTCF-dependent enhancer-blocking by alternative chromatin loop formation.

Authors:  Chunhui Hou; Hui Zhao; Keiji Tanimoto; Ann Dean
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-12       Impact factor: 11.205

Review 7.  Mediator of transcriptional regulation.

Authors:  L C Myers; R D Kornberg
Journal:  Annu Rev Biochem       Date:  2000       Impact factor: 23.643

8.  Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

Authors:  Suresh Cuddapah; Raja Jothi; Dustin E Schones; Tae-Young Roh; Kairong Cui; Keji Zhao
Journal:  Genome Res       Date:  2008-12-03       Impact factor: 9.043

Review 9.  A census of human transcription factors: function, expression and evolution.

Authors:  Juan M Vaquerizas; Sarah K Kummerfeld; Sarah A Teichmann; Nicholas M Luscombe
Journal:  Nat Rev Genet       Date:  2009-04       Impact factor: 53.242

10.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728
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  117 in total

Review 1.  The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis.

Authors:  Ali Shilatifard
Journal:  Annu Rev Biochem       Date:  2012       Impact factor: 23.643

2.  Discover regulatory DNA elements using chromatin signatures and artificial neural network.

Authors:  Hiram A Firpi; Duygu Ucar; Kai Tan
Journal:  Bioinformatics       Date:  2010-05-07       Impact factor: 6.937

3.  Transcription: Enhancers make non-coding RNA.

Authors:  Bing Ren
Journal:  Nature       Date:  2010-05-13       Impact factor: 49.962

4.  Construction of gene/transcription regulatory networks.

Authors:  Lisa Dailey
Journal:  Brief Funct Genomics       Date:  2010-01       Impact factor: 4.241

5.  Unraveling the score of the enhancer symphony.

Authors:  Thomas P Zwaka
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-06       Impact factor: 11.205

6.  Histone H3K27ac separates active from poised enhancers and predicts developmental state.

Authors:  Menno P Creyghton; Albert W Cheng; G Grant Welstead; Tristan Kooistra; Bryce W Carey; Eveline J Steine; Jacob Hanna; Michael A Lodato; Garrett M Frampton; Phillip A Sharp; Laurie A Boyer; Richard A Young; Rudolf Jaenisch
Journal:  Proc Natl Acad Sci U S A       Date:  2010-11-24       Impact factor: 11.205

7.  HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells.

Authors:  Jonathan E Reeder; Youn-Tae Kwak; Ryan P McNamara; Christian V Forst; Iván D'Orso
Journal:  Elife       Date:  2015-10-21       Impact factor: 8.140

8.  Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci.

Authors:  Michael L Stitzel; Praveen Sethupathy; Daniel S Pearson; Peter S Chines; Lingyun Song; Michael R Erdos; Ryan Welch; Stephen C J Parker; Alan P Boyle; Laura J Scott; Elliott H Margulies; Michael Boehnke; Terrence S Furey; Gregory E Crawford; Francis S Collins
Journal:  Cell Metab       Date:  2010-11-03       Impact factor: 27.287

9.  Genome-wide significant locus of beta-trace protein, a novel kidney function biomarker, identified in European and African Americans.

Authors:  Adrienne Tin; Brad C Astor; Eric Boerwinkle; Ron C Hoogeveen; Josef Coresh; W H Linda Kao
Journal:  Nephrol Dial Transplant       Date:  2013-01-16       Impact factor: 5.992

Review 10.  Complex genomic interactions in the dynamic regulation of transcription by the glucocorticoid receptor.

Authors:  Tina B Miranda; Stephanie A Morris; Gordon L Hager
Journal:  Mol Cell Endocrinol       Date:  2013-03-14       Impact factor: 4.102
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