Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration

Gavin M. Douglas, Michael D. Wilson, Alan M. Moses

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1 Cita (Scopus)

Resumen

Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift toward neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along a pseudogenized lineage: 1) Decreased transcription factor (TF) binding and 2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared with functional liver genes. However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in primate cis-regulatory modules may be obscured by background rates of TF binding site turnover.

Idioma originalEnglish
Páginas (desde-hasta)1478-1485
Número de páginas8
PublicaciónMolecular Biology and Evolution
Volumen33
N.º6
DOI
EstadoPublished - jun. 2 2016
Publicado de forma externa

Nota bibliográfica

Funding Information:
This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) through grants to A.M.M. and a fellowship to G.M.D. M.D.W. was funded by NSERC (436194-2013) and a Canada Research Chair. We thank Christopher Brown and an anonymous reviewer for suggesting the analysis of chromatin modification data

Publisher Copyright:
© 2016 The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

ASJC Scopus Subject Areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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