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Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

Martin, David I. K. and Singer, Meromit and Dhahbi, Joseph and Mao, Guanxiong and Zhang, Lu and Schroth, Gary P. and Pachter, Lior and Boffelli, Dario (2011) Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research, 21 (12). pp. 2049-2057. ISSN 1088-9051. PMCID PMC3227095. http://resolver.caltech.edu/CaltechAUTHORS:20170306-101015596

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Abstract

We have determined methylation state differences in the epigenomes of uncultured cells purified from human, chimpanzee, and orangutan, using digestion with a methylation-sensitive enzyme, deep sequencing, and computational analysis of the sequence data. The methylomes show a high degree of conservation, but the methylation states of approximately 10% of CpG island-like regions differ significantly between human and chimp. The differences are not associated with changes in CG content, and recapitulate the known phylogenetic relationship of the three species, indicating that they are stably maintained within each species. Inferences about the relationship between somatic and germline methylation states can be made by an analysis of CG decay, derived from methylation and sequence data. This indicates that somatic methylation states are highly related to germline states, and that the methylation differences between human and chimp have occurred in the germline. These results provide evidence for epigenetic changes that occur in the germline and distinguish closely related species, and suggest that germline epigenetic states might constrain somatic states.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://dx.doi.org/10.1101%2Fgr.122721.111DOIArticle
http://genome.cshlp.org/content/21/12/2049PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227095/PubMed CentralArticle
http://genome.cshlp.org/content/21/12/2049/suppl/DC1PublisherSupplemental Material
Additional Information:© 2011 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Received February 28, 2011; accepted in revised form September 6, 2011. This work was supported by NIH grants HL084474 (D.B.), ES016581 (D.I.K.M.), and CA115768 (D.I.K.M.). J.D. was supported by the California Institute of Regenerative Medicine. This study used biological materials obtained from the Southwest National Primate Research Center, which is supported by NIH-NCRR grant P51 RR013986. We thank Cole Trapnell for help with Bowtie alignments, and Cath Suter for helpful comments. Data access: The sequence data used in this study have been submitted to the NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE22376.
Funders:
Funding AgencyGrant Number
NIHHL084474
NIHES016581
NIHCA115768
California Institute for Regenerative Medicine (CIRM)UNSPECIFIED
NIHP51 RR013986
PubMed Central ID:PMC3227095
Record Number:CaltechAUTHORS:20170306-101015596
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20170306-101015596
Official Citation:Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states David I.K. Martin, Meromit Singer, Joseph Dhahbi, Guanxiong Mao, Lu Zhang, Gary P. Schroth, Lior Pachter, and Dario Boffelli Genome Res. December 2011 21: 2049-2057; Published in Advance September 9, 2011, doi:10.1101/gr.122721.111
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74770
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:06 Mar 2017 18:29
Last Modified:06 Mar 2017 18:29

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