Evidence for a common evolutionary rate in metazoan transcriptional networks

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Abstract

Genome sequences diverge more rapidly in mammals than in other animal lineages such as birds or insects. However, the effect of this rapid divergence on transcriptional evolution remains unclear. Recent reports have indicated a faster divergence of transcription factor binding in mammals than in insects, but others found the reverse for mRNA expression. Here, we show that these conflicting interpretations resulted from differing methodologies. We performed an integrated analysis of transcriptional network evolution by examining mRNA expression, transcription factor binding and cis-regulatory motifs across >25 animal species including mammals, birds and insects. Strikingly, we found that transcriptional networks evolve at a common rate across the three animal lineages. Furthermore, differences in rates of genome divergence were greatly reduced when restricting comparisons to chromatin-accessible sequences. The evolution of transcription is thus decoupled from the global rate of genome sequence evolution, suggesting that a small fraction of the genome regulates transcription.

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Anne-Ruxandra Carvunis

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Tina Wang

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Dylan Skola

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Alice Yu

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Jonathan Chen

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Jason F Kreisberg

Department of Medicine, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Trey Ideker

Department of Medicine, University of California, San Diego, La Jolla, United States

For correspondence
tideker@ucsd.edu

Competing interests
The authors declare that no competing interests exist.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.