Three periods of regulatory innovation during vertebrate evolution.

Journal Article (Journal Article)

The gain, loss, and modification of gene regulatory elements may underlie a substantial proportion of phenotypic changes on animal lineages. To investigate the gain of regulatory elements throughout vertebrate evolution, we identified genome-wide sets of putative regulatory regions for five vertebrates, including humans. These putative regulatory regions are conserved nonexonic elements (CNEEs), which are evolutionarily conserved yet do not overlap any coding or noncoding mature transcript. We then inferred the branch on which each CNEE came under selective constraint. Our analysis identified three extended periods in the evolution of gene regulatory elements. Early vertebrate evolution was characterized by regulatory gains near transcription factors and developmental genes, but this trend was replaced by innovations near extracellular signaling genes, and then innovations near posttranslational protein modifiers.

Full Text

Duke Authors

Cited Authors

  • Lowe, CB; Kellis, M; Siepel, A; Raney, BJ; Clamp, M; Salama, SR; Kingsley, DM; Lindblad-Toh, K; Haussler, D

Published Date

  • August 19, 2011

Published In

Volume / Issue

  • 333 / 6045

Start / End Page

  • 1019 - 1024

PubMed ID

  • 21852499

Pubmed Central ID

  • PMC3511857

Electronic International Standard Serial Number (EISSN)

  • 1095-9203

Digital Object Identifier (DOI)

  • 10.1126/science.1202702


  • eng

Conference Location

  • United States