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Status |
Public on Sep 05, 2019 |
Title |
Archaic and modern bone DNA methylation maps from the Neanderthal, Denisovan, modern human and chimpanzee |
Organisms |
Pan troglodytes; Homo sapiens |
Experiment type |
Methylation profiling by high throughput sequencing Third-party reanalysis
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Summary |
Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting 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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Overall design |
DNA methylation maps were reconstructed from several human groups, including two Neanderthals, one Denisovan and five anatomically modern humans (Ust Ishim, Stuttgart, Loschbour, I1583 and La Braña 1). Additionally, present-day DNA methylation maps were produced from two present-day human bones (WGBS) and two chimpanzee bones (WGBS and RRBS).
The metadata for the following samples are included in the supplementary file 'GSE96833_metadata_reanalysis_samples.xls': - Altai Neanderthal Reconstructed Methylome - Denisovan Reconstructed Methylome - Modern Human (Ust Ishim) Reconstructed Methylome - Modern Human (Stuttgart) Reconstructed Methylome - Modern Human (Loschbour) Reconstructed Methylome - Vindija Neanderthal Reconstructed Methylome
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Contributor(s) |
Carmel L, Gokhman D, Marques-Bonet T, Meissner A, Lalueza-Fox C, Reich D, Meshorer E, Pinhasi R, Vidal JM, Prada ME, Liebergall M, Kandel L, Mjungu D, Stone AC, Quillen EE, Bontrop R, Kondova I, Lipende I, Gelabert P, Ferrando-Bernal M, Gu H, Novak M, Alpaslan-Roodenberg S, Rohland N, Li H, Nieves-Colón MA, Mallick S, Nissim-Rafinia M, García-Pérez R, Housman G, Agranat-Tamir L |
Citation(s) |
31539495 |
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Submission date |
Mar 20, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
David Gokhman |
E-mail(s) |
david.gokhman@mail.huji.ac.il
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Organization name |
The Hebrew University of Jerusalem
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Street address |
Givat Ram, Safra Campus
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City |
Jerusalem |
ZIP/Postal code |
91904 |
Country |
Israel |
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Platforms (2) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
GPL16809 |
Illumina HiSeq 2000 (Pan troglodytes) |
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Samples (6)
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Relations |
BioProject |
PRJNA387623 |
SRA |
SRP107883 |
Supplementary file |
Size |
Download |
File type/resource |
GSE96833_Altai_Neanderthal_MethylationMap.bedgraph.gz |
156.8 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_Denisovan_MethylationMap.bedgraph.gz |
149.9 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_Loschbour_MethylationMap.bedgraph.gz |
153.5 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_RAW.tar |
789.1 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
GSE96833_Stuttgart_MethylationMap.bedgraph.gz |
155.0 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_Ust_Ishim_MethylationMap.bedgraph.gz |
157.3 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_Vindija_Neanderthal_MethylationMap.bedgraph.gz |
135.7 Mb |
(ftp)(http) |
BEDGRAPH |
GSE96833_metadata_reanalysis_samples.xls.gz |
7.7 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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