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Cell. 2015 Sep 24;163(1):68-83. doi: 10.1016/j.cell.2015.08.036. Epub 2015 Sep 10.

Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest.

Author information

1
Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
2
Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
3
Department of Cell and Developmental Biology, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
4
Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
5
Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: swigut@stanford.edu.
6
Department of Chemical and Systems Biology and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: wysocka@stanford.edu.

Abstract

cis-regulatory changes play a central role in morphological divergence, yet the regulatory principles underlying emergence of human traits remain poorly understood. Here, we use epigenomic profiling from human and chimpanzee cranial neural crest cells to systematically and quantitatively annotate divergence of craniofacial cis-regulatory landscapes. Epigenomic divergence is often attributable to genetic variation within TF motifs at orthologous enhancers, with a novel motif being most predictive of activity biases. We explore properties of this cis-regulatory change, revealing the role of particular retroelements, uncovering broad clusters of species-biased enhancers near genes associated with human facial variation, and demonstrating that cis-regulatory divergence is linked to quantitative expression differences of crucial neural crest regulators. Our work provides a wealth of candidates for future evolutionary studies and demonstrates the value of "cellular anthropology," a strategy of using in-vitro-derived embryonic cell types to elucidate both fundamental and evolving mechanisms underlying morphological variation in higher primates.

PMID:
26365491
PMCID:
PMC4848043
DOI:
10.1016/j.cell.2015.08.036
[Indexed for MEDLINE]
Free PMC Article

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