Literature DB >> 22705669

Comparative studies of gene expression and the evolution of gene regulation.

Irene Gallego Romero1, Ilya Ruvinsky, Yoav Gilad.   

Abstract

The hypothesis that differences in gene regulation have an important role in speciation and adaptation is more than 40 years old. With the advent of new sequencing technologies, we are able to characterize and study gene expression levels and associated regulatory mechanisms in a large number of individuals and species at an unprecedented resolution and scale. We have thus gained new insights into the evolutionary pressures that shape gene expression levels and have developed an appreciation for the relative importance of evolutionary changes in different regulatory genetic and epigenetic mechanisms. The current challenge is to link gene regulatory changes to adaptive evolution of complex phenotypes. Here we mainly focus on comparative studies in primates and how they are complemented by studies in model organisms.

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Year:  2012        PMID: 22705669      PMCID: PMC4034676          DOI: 10.1038/nrg3229

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


  116 in total

1.  Evolution of gene expression in the Drosophila melanogaster subgroup.

Authors:  Scott A Rifkin; Junhyong Kim; Kevin P White
Journal:  Nat Genet       Date:  2003-01-27       Impact factor: 38.330

2.  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

3.  optix drives the repeated convergent evolution of butterfly wing pattern mimicry.

Authors:  Robert D Reed; Riccardo Papa; Arnaud Martin; Heather M Hines; Brian A Counterman; Carolina Pardo-Diaz; Chris D Jiggins; Nicola L Chamberlain; Marcus R Kronforst; Rui Chen; Georg Halder; H Frederik Nijhout; W Owen McMillan
Journal:  Science       Date:  2011-07-21       Impact factor: 47.728

4.  Gene regulation for higher cells: a theory.

Authors:  R J Britten; E H Davidson
Journal:  Science       Date:  1969-07-25       Impact factor: 47.728

5.  teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance.

Authors:  J Doebley; A Stec; C Gustus
Journal:  Genetics       Date:  1995-09       Impact factor: 4.562

6.  Sex-specific and lineage-specific alternative splicing in primates.

Authors:  Ran Blekhman; John C Marioni; Paul Zumbo; Matthew Stephens; Yoav Gilad
Journal:  Genome Res       Date:  2009-12-15       Impact factor: 9.043

Review 7.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

Review 8.  Tempo and mode in evolution of transcriptional regulation.

Authors:  Kacy L Gordon; Ilya Ruvinsky
Journal:  PLoS Genet       Date:  2012-01-19       Impact factor: 5.917

9.  Evolution acts on enhancer organization to fine-tune gradient threshold readouts.

Authors:  Justin Crocker; Yoichiro Tamori; Albert Erives
Journal:  PLoS Biol       Date:  2008-11-04       Impact factor: 8.029

10.  Functional evolution of a cis-regulatory module.

Authors:  Michael Z Ludwig; Arnar Palsson; Elena Alekseeva; Casey M Bergman; Janaki Nathan; Martin Kreitman
Journal:  PLoS Biol       Date:  2005-03-15       Impact factor: 8.029

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  171 in total

Review 1.  Great ape genomics.

Authors:  Jeffrey D Wall
Journal:  ILAR J       Date:  2013

2.  Phylogenetic analysis of gene expression.

Authors:  Casey W Dunn; Xi Luo; Zhijin Wu
Journal:  Integr Comp Biol       Date:  2013-06-07       Impact factor: 3.326

3.  Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization.

Authors:  Lihua Zhang; Shihua Zhang
Journal:  Nucleic Acids Res       Date:  2019-07-26       Impact factor: 16.971

4.  Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes ( Crotalus cerastes).

Authors:  Rhett M Rautsaw; Erich P Hofmann; Mark J Margres; Matthew L Holding; Jason L Strickland; Andrew J Mason; Darin R Rokyta; Christopher L Parkinson
Journal:  Proc Biol Sci       Date:  2019-07-03       Impact factor: 5.349

5.  Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae.

Authors:  Marian Schubert; Lars Grønvold; Simen R Sandve; Torgeir R Hvidsten; Siri Fjellheim
Journal:  Plant Physiol       Date:  2019-03-08       Impact factor: 8.340

6.  Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae).

Authors:  Courtney N Passow; Anthony P Brown; Lenin Arias-Rodriguez; Muh-Ching Yee; Alexandra Sockell; Manfred Schartl; Wesley C Warren; Carlos Bustamante; Joanna L Kelley; Michael Tobler
Journal:  Mol Ecol       Date:  2017-07-04       Impact factor: 6.185

Review 7.  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

Review 8.  Human brain evolution: transcripts, metabolites and their regulators.

Authors:  Mehmet Somel; Xiling Liu; Philipp Khaitovich
Journal:  Nat Rev Neurosci       Date:  2013-01-17       Impact factor: 34.870

9.  Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures.

Authors:  Daniel H Chitwood; Julin N Maloof; Neelima R Sinha
Journal:  Plant Physiol       Date:  2013-04-12       Impact factor: 8.340

10.  A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.

Authors:  Junha Shin; Harald Marx; Alicia Richards; Dries Vaneechoutte; Dhileepkumar Jayaraman; Junko Maeda; Sanhita Chakraborty; Michael Sussman; Klaas Vandepoele; Jean-Michel Ané; Joshua Coon; Sushmita Roy
Journal:  Nucleic Acids Res       Date:  2021-01-11       Impact factor: 16.971

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