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

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

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.

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Bibliographic Details
Main Authors: Gokhman, David, Nissim-Rafinia, Malka, Agranat-Tamir, Lily, Housman, Genevieve, García-Pérez, Raquel, Lizano, Esther, Cheronet, Olivia, Mallick, Swapan, Nieves-Colón, Maria A., Li, Heng, Alpaslan-Roodenberg, Songül, Novak, Mario, Gu, Hongcang, Osinski, Jason M., Ferrando-Bernal, Manuel, Gelabert, Pere, Lipende, Iddi, Mjungu, Deus, Kondova, Ivanela, Bontrop, Ronald, Kullmer, Ottmar, Weber, Gerhard, Shahar, Tal, Dvir-Ginzberg, Mona, Faerman, Marina, Quillen, Ellen E., Meissner, Alexander, Lahav, Yonatan, Kandel, Leonid, Liebergall, Meir, Prada, María E., Vidal Encinas, Julio Manuel, Gronostajski, Richard M., Stone, Anne C., Yakir, Benjamin, Lalueza-Fox, Carles, Pinhasi, Ron, Reich, David, Marqués-Bonet, Tomàs, Meshorer, Eran, Carmel, Liran
Other Authors: Clore Israel Foundation
Format: artículo biblioteca
Language:English
Published: Springer Nature 2020-03-04
Online Access:http://hdl.handle.net/10261/218737
http://dx.doi.org/10.13039/100000001
http://dx.doi.org/10.13039/100000002
http://dx.doi.org/10.13039/501100003329
http://dx.doi.org/10.13039/100000011
http://dx.doi.org/10.13039/501100000780
http://dx.doi.org/10.13039/501100011033
http://dx.doi.org/10.13039/100000952
http://dx.doi.org/10.13039/501100000781
http://dx.doi.org/10.13039/100011084
http://dx.doi.org/10.13039/100001388
http://dx.doi.org/10.13039/501100002809
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Summary: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.

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