Comparative analysis of gene regulatory networks: from network reconstruction to evolution.

Annu Rev Cell Dev Biol
Authors
Keywords
Abstract

Regulation of gene expression is central to many biological processes. Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge. Comparative approaches that examine the conservation and divergence of circuits and their components across strains and species can help reconstruct circuits as well as provide insights into the evolution of gene regulatory processes and their adaptive contribution. In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequence to functional data. We highlight how these methods use evolutionary conservation and divergence to reliably detect regulatory components as well as estimate the extent and rate of divergence. Finally, we discuss the promise and open challenges in linking regulatory divergence to phenotypic divergence and adaptation.

Year of Publication
2015
Journal
Annu Rev Cell Dev Biol
Volume
31
Pages
399-428
Date Published
2015
ISSN
1530-8995
URL
DOI
10.1146/annurev-cellbio-100913-012908
PubMed ID
26355593
Links
Grant list
P50HG006193 / HG / NHGRI NIH HHS / United States
R01CA119176-01 / CA / NCI NIH HHS / United States
Howard Hughes Medical Institute / United States