Differential DNA methylation of vocal and facial anatomy genes in modern humans

Author:

Gokhman David,Nissim-Rafinia Malka,Agranat-Tamir Lily,Housman GenevieveORCID,García-Pérez Raquel,Lizano EstherORCID,Cheronet OliviaORCID,Mallick Swapan,Nieves-Colón Maria A.,Li Heng,Alpaslan-Roodenberg Songül,Novak Mario,Gu Hongcang,Osinski Jason M.,Ferrando-Bernal Manuel,Gelabert PereORCID,Lipende Iddi,Mjungu Deus,Kondova IvanelaORCID,Bontrop RonaldORCID,Kullmer OttmarORCID,Weber Gerhard,Shahar Tal,Dvir-Ginzberg MonaORCID,Faerman Marina,Quillen Ellen E.,Meissner AlexanderORCID,Lahav Yonatan,Kandel Leonid,Liebergall Meir,Prada María E.,Vidal Julio M.ORCID,Gronostajski Richard M.ORCID,Stone Anne C.ORCID,Yakir Benjamin,Lalueza-Fox CarlesORCID,Pinhasi RonORCID,Reich DavidORCID,Marques-Bonet TomasORCID,Meshorer EranORCID,Carmel LiranORCID

Abstract

AbstractChanges in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry

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