Literature DB >> 25215415

Comparative studies of gene regulatory mechanisms.

Athma A Pai1, Yoav Gilad2.   

Abstract

It has become increasingly clear that changes in gene regulation have played an important role in adaptive evolution both between and within species. Over the past five years, comparative studies have moved beyond simple characterizations of differences in gene expression levels within and between species to studying variation in regulatory mechanisms. We still know relatively little about the precise chain of events that lead to most regulatory adaptations, but we have taken significant steps towards understanding the relative importance of changes in different mechanisms of gene regulatory evolution. In this review, we first discuss insights from comparative studies in model organisms, where the available experimental toolkit is extensive. We then focus on a few recent comparative studies in primates, where the limited feasibility of experimental manipulation dictates the approaches that can be used to study gene regulatory evolution.
Copyright © 2014 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Year:  2014        PMID: 25215415      PMCID: PMC4258459          DOI: 10.1016/j.gde.2014.08.010

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


  45 in total

1.  Generation of a novel wing colour pattern by the Wingless morphogen.

Authors:  Thomas Werner; Shigeyuki Koshikawa; Thomas M Williams; Sean B Carroll
Journal:  Nature       Date:  2010-04-07       Impact factor: 49.962

2.  Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

Authors:  Roger Pique-Regi; Jacob F Degner; Athma A Pai; Daniel J Gaffney; Yoav Gilad; Jonathan K Pritchard
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

3.  High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Authors:  Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

4.  Segmental duplications contribute to gene expression differences between humans and chimpanzees.

Authors:  Ran Blekhman; Alicia Oshlack; Yoav Gilad
Journal:  Genetics       Date:  2009-03-30       Impact factor: 4.562

5.  Regulatory divergence in Drosophila revealed by mRNA-seq.

Authors:  C Joel McManus; Joseph D Coolon; Michael O Duff; Jodi Eipper-Mains; Brenton R Graveley; Patricia J Wittkopp
Journal:  Genome Res       Date:  2010-03-30       Impact factor: 9.043

6.  Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.

Authors:  Yingguang Frank Chan; Melissa E Marks; Felicity C Jones; Guadalupe Villarreal; Michael D Shapiro; Shannon D Brady; Audrey M Southwick; Devin M Absher; Jane Grimwood; Jeremy Schmutz; Richard M Myers; Dmitri Petrov; Bjarni Jónsson; Dolph Schluter; Michael A Bell; David M Kingsley
Journal:  Science       Date:  2009-12-10       Impact factor: 47.728

7.  Human-specific gain of function in a developmental enhancer.

Authors:  Shyam Prabhakar; Axel Visel; Jennifer A Akiyama; Malak Shoukry; Keith D Lewis; Amy Holt; Ingrid Plajzer-Frick; Harris Morrison; David R Fitzpatrick; Veena Afzal; Len A Pennacchio; Edward M Rubin; James P Noonan
Journal:  Science       Date:  2008-09-05       Impact factor: 47.728

8.  The evolution of gene regulation underlies a morphological difference between two Drosophila sister species.

Authors:  Sangyun Jeong; Mark Rebeiz; Peter Andolfatto; Thomas Werner; John True; Sean B Carroll
Journal:  Cell       Date:  2008-03-07       Impact factor: 41.582

9.  Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.

Authors:  Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenez; Sarah Mackay; Iannis Talianidis; Paul Flicek; Duncan T Odom
Journal:  Science       Date:  2010-04-08       Impact factor: 47.728

10.  A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

Authors:  Athma A Pai; Jordana T Bell; John C Marioni; Jonathan K Pritchard; Yoav Gilad
Journal:  PLoS Genet       Date:  2011-02-24       Impact factor: 5.917

View more
  8 in total

Review 1.  Comparative transcriptomics in human and mouse.

Authors:  Alessandra Breschi; Thomas R Gingeras; Roderic Guigó
Journal:  Nat Rev Genet       Date:  2017-05-08       Impact factor: 53.242

2.  Evolution of DNA Methylation in Papio Baboons.

Authors:  Tauras P Vilgalys; Jeffrey Rogers; Clifford J Jolly; Sayan Mukherjee; Jenny Tung
Journal:  Mol Biol Evol       Date:  2019-03-01       Impact factor: 16.240

Review 3.  The evolution of the human genome.

Authors:  Corinne N Simonti; John A Capra
Journal:  Curr Opin Genet Dev       Date:  2015-09-09       Impact factor: 5.578

Review 4.  Prime time for primate functional genomics.

Authors:  Genevieve Housman; Yoav Gilad
Journal:  Curr Opin Genet Dev       Date:  2020-06-13       Impact factor: 5.578

5.  Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.

Authors:  David Martín-Gálvez; Denis Dunoyer de Segonzac; Man Chun John Ma; Anne E Kwitek; David Thybert; Paul Flicek
Journal:  BMC Genomics       Date:  2017-12-22       Impact factor: 3.969

6.  Statistical modelling of CG interdistance across multiple organisms.

Authors:  Merlotti A; Faria do Valle I; Castellani G; Remondini D
Journal:  BMC Bioinformatics       Date:  2018-10-15       Impact factor: 3.169

7.  Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species.

Authors:  Ehsan Pashay Ahi; Florian Richter; Laurène Alicia Lecaudey; Kristina M Sefc
Journal:  Sci Rep       Date:  2019-06-21       Impact factor: 4.379

Review 8.  The regulatory landscape of neurite development in Caenorhabditis elegans.

Authors:  Rasoul Godini; Hossein Fallahi; Roger Pocock
Journal:  Front Mol Neurosci       Date:  2022-08-25       Impact factor: 6.261

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.