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

David Gokhman, Malka Nissim-Rafinia, Lily Agranat-Tamir, Genevieve Housman, Raquel García-Pérez, Esther Lizano, Olivia Cheronet, Swapan Mallick, Maria A. Nieves-Colón, Heng Li, Songül Alpaslan-Roodenberg, Mario Novak, Hongcang Gu, Jason M. Osinski, Manuel Ferrando-Bernal, Pere Gelabert, Iddi Lipende, Deus Mjungu, Ivanela Kondova, Ronald BontropOttmar Kullmer, Gerhard Weber, Tal Shahar, Mona Dvir-Ginzberg, Marina Faerman, Ellen E. Quillen, Alexander Meissner, Yonatan Lahav, Leonid Kandel, Meir Liebergall, María E. Prada, Julio M. Vidal, Richard M. Gronostajski, Anne C. Stone, Benjamin Yakir, Carles Lalueza-Fox, Ron Pinhasi, David Reich, Tomas Marques-Bonet, Eran Meshorer, Liran Carmel

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

Changes 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.

Original languageEnglish (US)
Article number1189
JournalNature communications
Volume11
Issue number1
DOIs
StatePublished - Dec 1 2020

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Gokhman, D., Nissim-Rafinia, M., Agranat-Tamir, L., Housman, G., García-Pérez, R., Lizano, E., Cheronet, O., Mallick, S., Nieves-Colón, M. A., Li, H., Alpaslan-Roodenberg, S., Novak, M., Gu, H., Osinski, J. M., Ferrando-Bernal, M., Gelabert, P., Lipende, I., Mjungu, D., Kondova, I., ... Carmel, L. (2020). Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nature communications, 11(1), [1189]. https://doi.org/10.1038/s41467-020-15020-6