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 Bontrop; Ottmar 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

doi:10.1038/s41467-020-15020-6

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

47 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 language	English
Article number	1189
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-15020-6
State	Published - 1 Dec 2020

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Publisher Copyright:
© 2020, The Author(s).

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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), Article 1189. https://doi.org/10.1038/s41467-020-15020-6

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title = "Differential DNA methylation of vocal and facial anatomy genes in modern humans",

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.",

author = "David Gokhman and Malka Nissim-Rafinia and Lily Agranat-Tamir and Genevieve Housman and Raquel Garc{\'i}a-P{\'e}rez and Esther Lizano and Olivia Cheronet and Swapan Mallick and Nieves-Col{\'o}n, {Maria A.} and Heng Li and Song{\"u}l Alpaslan-Roodenberg and Mario Novak and Hongcang Gu and Osinski, {Jason M.} and Manuel Ferrando-Bernal and Pere Gelabert and Iddi Lipende and Deus Mjungu and Ivanela Kondova and Ronald Bontrop and Ottmar Kullmer and Gerhard Weber and Tal Shahar and Mona Dvir-Ginzberg and Marina Faerman and Quillen, {Ellen E.} and Alexander Meissner and Yonatan Lahav and Leonid Kandel and Meir Liebergall and Prada, {Mar{\'i}a E.} and Vidal, {Julio M.} and Gronostajski, {Richard M.} and Stone, {Anne C.} and Benjamin Yakir and Carles Lalueza-Fox and Ron Pinhasi and David Reich and Tomas Marques-Bonet and Eran Meshorer and Liran Carmel",

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year = "2020",

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doi = "10.1038/s41467-020-15020-6",

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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, MA, Li, H, Alpaslan-Roodenberg, S, Novak, M, Gu, H, Osinski, JM, Ferrando-Bernal, M, Gelabert, P, Lipende, I, Mjungu, D, Kondova, I, Bontrop, R, Kullmer, O, Weber, G, Shahar, T, Dvir-Ginzberg, M, Faerman, M, Quillen, EE, Meissner, A, Lahav, Y, Kandel, L, Liebergall, M, Prada, ME, Vidal, JM, Gronostajski, RM, Stone, AC, Yakir, B, Lalueza-Fox, C, Pinhasi, R, Reich, D, Marques-Bonet, T, Meshorer, E & Carmel, L 2020, 'Differential DNA methylation of vocal and facial anatomy genes in modern humans', Nature Communications, vol. 11, no. 1, 1189. https://doi.org/10.1038/s41467-020-15020-6

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AU - Gokhman, David

AU - Nissim-Rafinia, Malka

AU - Agranat-Tamir, Lily

AU - Housman, Genevieve

AU - García-Pérez, Raquel

AU - Lizano, Esther

AU - Cheronet, Olivia

AU - Mallick, Swapan

AU - Nieves-Colón, Maria A.

AU - Li, Heng

AU - Alpaslan-Roodenberg, Songül

AU - Novak, Mario

AU - Gu, Hongcang

AU - Osinski, Jason M.

AU - Ferrando-Bernal, Manuel

AU - Gelabert, Pere

AU - Lipende, Iddi

AU - Mjungu, Deus

AU - Kondova, Ivanela

AU - Bontrop, Ronald

AU - Kullmer, Ottmar

AU - Weber, Gerhard

AU - Shahar, Tal

AU - Dvir-Ginzberg, Mona

AU - Faerman, Marina

AU - Quillen, Ellen E.

AU - Meissner, Alexander

AU - Lahav, Yonatan

AU - Kandel, Leonid

AU - Liebergall, Meir

AU - Prada, María E.

AU - Vidal, Julio M.

AU - Gronostajski, Richard M.

AU - Stone, Anne C.

AU - Yakir, Benjamin

AU - Lalueza-Fox, Carles

AU - Pinhasi, Ron

AU - Reich, David

AU - Marques-Bonet, Tomas

AU - Meshorer, Eran

AU - Carmel, Liran

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

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