Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Marit W Vermunt, Sander C Tan, Bas Castelijns, Geert Geeven, Peter Reinink, Ewart de Bruijn, Ivanela Kondova, Stephan Persengiev, Ronald Bontrop, Edwin Cuppen, Wouter de Laat, Menno P Creyghton,

Research output: Contribution to journal/periodicalArticleScientificpeer-review

Abstract

Although genome sequencing has identified numerous noncoding alterations between primate species, which of those are regulatory and potentially relevant to the evolution of the human brain is unclear. Here we annotated cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genomes using chromatin immunoprecipitation followed by sequencing (ChIP-seq) in different anatomical regions of the adult brain. We found high similarity in the genomic positioning of rhesus macaque and human CREs, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. Most of the observed regulatory changes between humans and rhesus macaques occurred before the ancestral separation of humans and chimpanzees, leaving a modest set of regulatory elements with predicted human specificity. Our data refine previous predictions and hypotheses on the consequences of genomic changes between primate species and allow the identification of regulatory alterations relevant to the evolution of the brain.

Original languageEnglish
Pages (from-to)494-503
Number of pages10
JournalNature Neuroscience
Volume19
Issue number3
DOIs
Publication statusPublished - Mar 2016

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    Vermunt, M. W., Tan, S. C., Castelijns, B., Geeven, G., Reinink, P., de Bruijn, E., Kondova, I., Persengiev, S., Bontrop, R., Cuppen, E., de Laat, W., Creyghton, M. P. (2016). Epigenomic annotation of gene regulatory alterations during evolution of the primate brain. Nature Neuroscience, 19(3), 494-503. https://doi.org/10.1038/nn.4229