Literature DB >> 23503198

Enhancers: five essential questions.

Len A Pennacchio1, Wendy Bickmore, Ann Dean, Marcelo A Nobrega, Gill Bejerano.   

Abstract

It is estimated that the human genome contains hundreds of thousands of enhancers, so understanding these gene-regulatory elements is a crucial goal. Several fundamental questions need to be addressed about enhancers, such as how do we identify them all, how do they work, and how do they contribute to disease and evolution? Five prominent researchers in this field look at how much we know already and what needs to be done to answer these questions.

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Year:  2013        PMID: 23503198      PMCID: PMC4445073          DOI: 10.1038/nrg3458

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


  74 in total

Review 1.  Long-range gene control and genetic disease.

Authors:  Dirk A Kleinjan; Laura A Lettice
Journal:  Adv Genet       Date:  2008       Impact factor: 1.944

2.  Ultraconservation identifies a small subset of extremely constrained developmental enhancers.

Authors:  Axel Visel; Shyam Prabhakar; Jennifer A Akiyama; Malak Shoukry; Keith D Lewis; Amy Holt; Ingrid Plajzer-Frick; Veena Afzal; Edward M Rubin; Len A Pennacchio
Journal:  Nat Genet       Date:  2008-01-06       Impact factor: 38.330

3.  Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution.

Authors:  Sean B Carroll
Journal:  Cell       Date:  2008-07-11       Impact factor: 41.582

4.  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

5.  Dispensability of mammalian DNA.

Authors:  Cory McLean; Gill Bejerano
Journal:  Genome Res       Date:  2008-10-02       Impact factor: 9.043

6.  The mediator complex functions as a coactivator for GATA-1 in erythropoiesis via subunit Med1/TRAP220.

Authors:  Melanie Stumpf; Claudia Waskow; Marit Krötschel; Dominic van Essen; Patrick Rodriguez; Xiaoting Zhang; Boris Guyot; Robert G Roeder; Tilman Borggrefe
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-28       Impact factor: 11.205

7.  The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation.

Authors:  Tobias Ragoczy; M A Bender; Agnes Telling; Rachel Byron; Mark Groudine
Journal:  Genes Dev       Date:  2006-05-16       Impact factor: 11.361

8.  In vivo enhancer analysis of human conserved non-coding sequences.

Authors:  Len A Pennacchio; Nadav Ahituv; Alan M Moses; Shyam Prabhakar; Marcelo A Nobrega; Malak Shoukry; Simon Minovitsky; Inna Dubchak; Amy Holt; Keith D Lewis; Ingrid Plajzer-Frick; Jennifer Akiyama; Sarah De Val; Veena Afzal; Brian L Black; Olivier Couronne; Michael B Eisen; Axel Visel; Edward M Rubin
Journal:  Nature       Date:  2006-11-05       Impact factor: 49.962

9.  An atomic model of the interferon-beta enhanceosome.

Authors:  Daniel Panne; Tom Maniatis; Stephen C Harrison
Journal:  Cell       Date:  2007-06-15       Impact factor: 41.582

10.  ChIP-seq accurately predicts tissue-specific activity of enhancers.

Authors:  Axel Visel; Matthew J Blow; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; Bing Ren; Edward M Rubin; Len A Pennacchio
Journal:  Nature       Date:  2009-02-12       Impact factor: 49.962

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  201 in total

Review 1.  Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.

Authors:  Julieta Aprea; Federico Calegari
Journal:  EMBO J       Date:  2015-10-29       Impact factor: 11.598

2.  Sorting Out Identities: An Educational Primer for Use with "Novel Tools for Genetic Manipulation of Follicle Stem Cells in the Drosophila Ovary Reveal an Integrin-Dependent Transition from Quiescence to Proliferation".

Authors:  Diane Silva; Jennifer C Jemc
Journal:  Genetics       Date:  2015-09       Impact factor: 4.562

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.  Enhancer mutations and phenotype modularity.

Authors:  Christopher T Gordon; Stanislas Lyonnet
Journal:  Nat Genet       Date:  2014-01       Impact factor: 38.330

5.  Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants.

Authors:  Lang Wu; Jifeng Wang; Qiuyin Cai; Taylor B Cavazos; Nima C Emami; Jirong Long; Xiao-Ou Shu; Yingchang Lu; Xingyi Guo; Joshua A Bauer; Bogdan Pasaniuc; Kathryn L Penney; Matthew L Freedman; Zsofia Kote-Jarai; John S Witte; Christopher A Haiman; Rosalind A Eeles; Wei Zheng
Journal:  Cancer Res       Date:  2019-05-17       Impact factor: 12.701

6.  Epigenomic profiling reveals an association between persistence of DNA methylation and metabolic memory in the DCCT/EDIC type 1 diabetes cohort.

Authors:  Zhuo Chen; Feng Miao; Andrew D Paterson; John M Lachin; Lingxiao Zhang; Dustin E Schones; Xiwei Wu; Jinhui Wang; Joshua D Tompkins; Saul Genuth; Barbara H Braffett; Arthur D Riggs; Rama Natarajan
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-09       Impact factor: 11.205

Review 7.  Architectural proteins, transcription, and the three-dimensional organization of the genome.

Authors:  Caelin Cubeñas-Potts; Victor G Corces
Journal:  FEBS Lett       Date:  2015-05-22       Impact factor: 4.124

8.  Restraining the enhancers from straying.

Authors:  Rakesh K Mishra
Journal:  J Biosci       Date:  2014-12       Impact factor: 1.826

9.  Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.

Authors:  Anusha Nagari; Shino Murakami; Venkat S Malladi; W Lee Kraus
Journal:  Methods Mol Biol       Date:  2017

10.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

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