Literature DB >> 25764334

Variation in vertebrate cis-regulatory elements in evolution and disease.

Adam Thomas Douglas1, Robert D Hill.   

Abstract

Much of the genetic information that drives animal diversity lies within the vast non-coding regions of the genome. Multi-species sequence conservation in non-coding regions of the genome flags important regulatory elements and more recently, techniques that look for functional signatures predicted for regulatory sequences have added to the identification of thousands more. For some time, biologists have argued that changes in cis-regulatory sequences creates the basic genetic framework for evolutionary change. Recent advances support this notion and show that there is extensive genomic variability in non-coding regulatory elements associated with trait variation, speciation and disease.

Entities:  

Keywords:  Non-coding conserved elements; archipelagos; enhancers; evolution; holoenhancers; regulatory mutations

Mesh:

Year:  2014        PMID: 25764334      PMCID: PMC4215174          DOI: 10.4161/trns.28848

Source DB:  PubMed          Journal:  Transcription        ISSN: 2154-1272


  73 in total

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Authors:  James P Noonan; Andrew S McCallion
Journal:  Annu Rev Genomics Hum Genet       Date:  2010       Impact factor: 8.929

2.  A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns.

Authors:  Tomislav Domazet-Lošo; Diethard Tautz
Journal:  Nature       Date:  2010-12-09       Impact factor: 49.962

3.  ChIP-Seq identification of weakly conserved heart enhancers.

Authors:  Matthew J Blow; David J McCulley; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; James Bristow; Bing Ren; Brian L Black; Edward M Rubin; Axel Visel; Len A Pennacchio
Journal:  Nat Genet       Date:  2010-08-22       Impact factor: 38.330

Review 4.  Functional and mechanistic diversity of distal transcription enhancers.

Authors:  Michael Bulger; Mark Groudine
Journal:  Cell       Date:  2011-02-04       Impact factor: 41.582

5.  Transcriptional enhancers in animal development and evolution.

Authors:  Mike Levine
Journal:  Curr Biol       Date:  2010-09-14       Impact factor: 10.834

6.  A novel regulatory element for Shh expression in the lung and gut of mouse embryos.

Authors:  Nagaharu Tsukiji; Takanori Amano; Toshihiko Shiroishi
Journal:  Mech Dev       Date:  2013-10-22       Impact factor: 1.882

7.  A unique chromatin signature uncovers early developmental enhancers in humans.

Authors:  Alvaro Rada-Iglesias; Ruchi Bajpai; Tomek Swigut; Samantha A Brugmann; Ryan A Flynn; Joanna Wysocka
Journal:  Nature       Date:  2010-12-15       Impact factor: 49.962

8.  An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape.

Authors:  Mirna Marinić; Tugce Aktas; Sandra Ruf; François Spitz
Journal:  Dev Cell       Date:  2013-02-28       Impact factor: 12.270

9.  Nucleosome dynamics define transcriptional enhancers.

Authors:  Housheng Hansen He; Clifford A Meyer; Hyunjin Shin; Shannon T Bailey; Gang Wei; Qianben Wang; Yong Zhang; Kexin Xu; Min Ni; Mathieu Lupien; Piotr Mieczkowski; Jason D Lieb; Keji Zhao; Myles Brown; X Shirley Liu
Journal:  Nat Genet       Date:  2010-03-07       Impact factor: 38.330

10.  Human-specific loss of regulatory DNA and the evolution of human-specific traits.

Authors:  Cory Y McLean; Philip L Reno; Alex A Pollen; Abraham I Bassan; Terence D Capellini; Catherine Guenther; Vahan B Indjeian; Xinhong Lim; Douglas B Menke; Bruce T Schaar; Aaron M Wenger; Gill Bejerano; David M Kingsley
Journal:  Nature       Date:  2011-03-10       Impact factor: 49.962

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  9 in total

1.  Towards a map of cis-regulatory sequences in the human genome.

Authors:  Meng Niu; Ehsan Tabari; Pengyu Ni; Zhengchang Su
Journal:  Nucleic Acids Res       Date:  2018-06-20       Impact factor: 16.971

2.  Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers.

Authors:  Irfan Hussain; Rabail Zehra Raza; Shahid Ali; Muhammad Abrar; Amir Ali Abbasi
Journal:  Dev Genes Evol       Date:  2021-03-02       Impact factor: 0.900

3.  The neural crest/domestication syndrome hypothesis, explained: reply to Johnsson, Henriksen, and Wright.

Authors:  Adam S Wilkins; Richard Wrangham; W Tecumseh Fitch
Journal:  Genetics       Date:  2021-08-26       Impact factor: 4.402

Review 4.  The Myth of Optimality in Clinical Neuroscience.

Authors:  Avram J Holmes; Lauren M Patrick
Journal:  Trends Cogn Sci       Date:  2018-02-20       Impact factor: 20.229

5.  An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax).

Authors:  Massimiliano Babbucci; Serena Ferraresso; Marianna Pauletto; Rafaella Franch; Chiara Papetti; Tomaso Patarnello; Paolo Carnier; Luca Bargelloni
Journal:  Sci Rep       Date:  2016-12-08       Impact factor: 4.379

6.  SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile.

Authors:  Sara Pegolo; Christos Dadousis; Núria Mach; Yuliaxis Ramayo-Caldas; Marcello Mele; Giuseppe Conte; Stefano Schiavon; Giovanni Bittante; Alessio Cecchinato
Journal:  Sci Rep       Date:  2017-12-11       Impact factor: 4.379

7.  Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat.

Authors:  Minako Yoshihara; Daisuke Saito; Tetsuya Sato; Osamu Ohara; Takashi Kuramoto; Mikita Suyama
Journal:  BMC Genomics       Date:  2016-08-09       Impact factor: 3.969

8.  Potassium Channel-Associated Bioelectricity of the Dermomyotome Determines Fin Patterning in Zebrafish.

Authors:  Martin R Silic; Qiuyu Wu; Brian H Kim; Greg Golling; Kenny H Chen; Renata Freitas; Alexander A Chubykin; Suresh K Mittal; GuangJun Zhang
Journal:  Genetics       Date:  2020-06-16       Impact factor: 4.562

9.  Evolution of mouse circadian enhancers from transposable elements.

Authors:  Julius Judd; Hayley Sanderson; Cédric Feschotte
Journal:  Genome Biol       Date:  2021-06-29       Impact factor: 13.583

  9 in total

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