Comparative studies of gene expression and the evolution of gene regulation

IG Romero, I Ruvinsky, Y Gilad - Nature Reviews Genetics, 2012 - nature.com
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 …

The evolution of transcriptional regulation in eukaryotes

GA Wray, MW Hahn, E Abouheif… - Molecular biology …, 2003 - academic.oup.com
Gene expression is central to the genotype-phenotype relationship in all organisms, and it is
an important component of the genetic basis for evolutionary change in diverse aspects of …

Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

H Suresh, M Crow, N Jorstad, R Hodge… - Nature Ecology & …, 2023 - nature.com
Enhanced cognitive function in humans is hypothesized to result from cortical expansion
and increased cellular diversity. However, the mechanisms that drive these phenotypic …

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

JC Marioni, CE Mason, SM Mane, M Stephens… - Genome …, 2008 - genome.cshlp.org
Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for
genotyping, analysis of methylation patterns, and identification of transcription factor binding …

Evidence for dynamically organized modularity in the yeast protein–protein interaction network

JDJ Han, N Bertin, T Hao, DS Goldberg, GF Berriz… - Nature, 2004 - nature.com
In apparently scale-free protein–protein interaction networks, or 'interactome'networks,, most
proteins interact with few partners, whereas a small but significant proportion of proteins, the …

Evolutionary changes in cis and trans gene regulation

PJ Wittkopp, BK Haerum, AG Clark - Nature, 2004 - nature.com
Differences in gene expression are central to evolution. Such differences can arise from cis-
regulatory changes that affect transcription initiation, transcription rate and/or transcript …

Detecting signatures of selection on gene expression

PD Price, DH Palmer Droguett, JA Taylor… - Nature Ecology & …, 2022 - nature.com
A substantial amount of phenotypic diversity results from changes in gene expression levels
and patterns. Understanding how the transcriptome evolves is therefore a key priority in …

Evolutionary genetics of genome merger and doubling in plants

JJ Doyle, LE Flagel, AH Paterson… - Annual review of …, 2008 - annualreviews.org
Polyploidy is a common mode of evolution in flowering plants. The profound effects of
polyploidy on gene expression appear to be caused more by hybridity than by genome …

Gene expression divergence recapitulates the developmental hourglass model

AT Kalinka, KM Varga, DT Gerrard, S Preibisch… - Nature, 2010 - nature.com
The observation that animal morphology tends to be conserved during the embryonic
phylotypic period (a period of maximal similarity between the species within each animal …

Regulatory divergence in Drosophila revealed by mRNA-seq

CJ McManus, JD Coolon, MO Duff… - Genome …, 2010 - genome.cshlp.org
The regulation of gene expression is critical for organismal function and is an important
source of phenotypic diversity between species. Understanding the genetic and molecular …