{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T09:48:23Z","timestamp":1716889703325},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1576,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivations: High-throughput sequencing has made it possible to sequence DNA methylation of a whole genome at the single-base resolution. A sample, however, may contain a number of distinct methylation patterns. For instance, cells of different types and in different developmental stages may have different methylation patterns. Alleles may be differentially methylated, which may partially explain that the large portions of epigenomes from single cell types are partially methylated, and may have major effects on transcriptional output. Approaches relying on DNA sequence polymorphism to identify individual patterns from a mixture of heterogeneous epigenomes are insufficient as methylcytosines occur at a much higher density than SNPs.<\/jats:p><jats:p>Results: We have developed a mixture model-based approach for resolving distinct epigenomes from a heterogeneous sample. In particular, the model is applied to the detection of allele-specific methylation (ASM). The methods are tested on a synthetic methylome and applied to an Arabidopsis single root cell methylome.<\/jats:p><jats:p>Contact: \u00a0qpeng@cs.ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts231","type":"journal-article","created":{"date-parts":[[2012,6,11]],"date-time":"2012-06-11T14:09:18Z","timestamp":1339423758000},"page":"i163-i171","source":"Crossref","is-referenced-by-count":20,"title":["Detection of allele-specific methylation through a generalized heterogeneous epigenome model"],"prefix":"10.1093","volume":"28","author":[{"given":"Qian","family":"Peng","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093 and 2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA"},{"name":"1 Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093 and 2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph R.","family":"Ecker","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093 and 2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA"},{"name":"1 Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093 and 2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA"},{"name":"1 Department of Computer Science and Engineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093 and 2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. 4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"2023012512325988800_B1","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1093\/hmg\/9.16.2395","article-title":"The DNA methyltransferases of mammals","volume":"9","author":"Bestor","year":"2000","journal-title":"Hum. Mol. Genet."},{"key":"2023012512325988800_B2","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature06745","article-title":"Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning","volume":"452","author":"Cokus","year":"2008","journal-title":"Nature"},{"key":"2023012512325988800_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.2517-6161.1977.tb01600.x","article-title":"Maximum likelihood from incomplete data via the EM algorithm","volume":"39","author":"Dempster","year":"1977","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012512325988800_B4","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1126\/science.1136352","article-title":"Gene body-specific methylation on the active X chromosome","volume":"315","author":"Hellman","year":"2007","journal-title":"Science"},{"key":"2023012512325988800_B5","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1093\/nar\/29.1.102","article-title":"The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant","volume":"29","author":"Huala","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012512325988800_B6","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ng.174","article-title":"Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation","volume":"40","author":"Kerkel","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012512325988800_B7","doi-asserted-by":"crossref","first-page":"17739","DOI":"10.1073\/pnas.0503976102","article-title":"Counting human somatic cell replications: Methylation mirrors endometrial stem cell divisions","volume":"102","author":"Kim","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012512325988800_B8","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/nrc1045","article-title":"The power and the promise of DNA methylation markers","volume":"3","author":"Laird","year":"2003","journal-title":"Nat. Rev. Cancer"},{"key":"2023012512325988800_B9","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/0092-8674(92)90611-F","article-title":"Targeted mutation of the DNA methyltransferase gene results in embryonic lethality","volume":"69","author":"Li","year":"1992","journal-title":"Cell"},{"key":"2023012512325988800_B10","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nature02651","article-title":"Role of transposable elements in heterochromatin and epigenetic control","volume":"430","author":"Lippman","year":"2004","journal-title":"Nature"},{"key":"2023012512325988800_B11","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1101\/gr.083451.108","article-title":"Finding the fifth base: Genome-wide sequencing of cytosine methylation","volume":"19","author":"Lister","year":"2009","journal-title":"Genome Res."},{"key":"2023012512325988800_B12","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.cell.2008.03.029","article-title":"Highly integrated single-base resolution maps of the epigenome in Arabidopsis","volume":"133","author":"Lister","year":"2008","journal-title":"Cell"},{"key":"2023012512325988800_B13","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nature08514","article-title":"Human DNA methylomes at base resolution show widespread epigenomic differences","volume":"462","author":"Lister","year":"2009","journal-title":"Nature"},{"key":"2023012512325988800_B14","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2229-11-113","article-title":"Identification of imprinted genes subject to parent-of-origin specific expression in arabidopsis thaliana seeds","volume":"11","author":"McKeown","year":"2011","journal-title":"BMC Plant Biol."},{"key":"2023012512325988800_B15","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/nature07107","article-title":"Genome-scale DNA methylation maps of pluripotent and differentiated cells","volume":"454","author":"Meissner","year":"2008","journal-title":"Nature"},{"key":"2023012512325988800_B16","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1126\/science.1180677","article-title":"The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana","volume":"327","author":"Ossowski","year":"2010","journal-title":"Science"},{"key":"2023012512325988800_B17","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/416552a","article-title":"DNMT1 and DNMT3b cooperate to silence genes in human cancer cells","volume":"416","author":"Rhee","year":"2002","journal-title":"Nature"},{"key":"2023012512325988800_B18","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1159\/000130315","article-title":"X inactivation, differentiation, and DNA methylation","volume":"14","author":"Riggs","year":"1975","journal-title":"Cytogenet. Cell Genet."},{"key":"2023012512325988800_B19","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1126\/science.1212959","article-title":"Transgenerational epigenetic instability is a source of novel methylation variants","volume":"334","author":"Schmitz","year":"2011","journal-title":"Science"},{"key":"2023012512325988800_B20","doi-asserted-by":"crossref","first-page":"610","DOI":"10.4161\/cc.5.6.2570","article-title":"Counting divisions in a human somatic cell tree: How, what and why?","volume":"5","author":"Shibata","year":"2006","journal-title":"Cell Cycle"},{"key":"2023012512325988800_B21","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1101\/gr.104695.109","article-title":"Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome","volume":"20","author":"Shoemaker","year":"2010","journal-title":"Genome Res."},{"key":"2023012512325988800_B22","doi-asserted-by":"crossref","first-page":"10839","DOI":"10.1073\/pnas.191225998","article-title":"Investigating stem cells in human colon by using methylation patterns","volume":"98","author":"Yatabe","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012512325988800_B23","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1016\/j.cell.2006.08.003","article-title":"Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis","volume":"126","author":"Zhang","year":"2006","journal-title":"Cell"},{"key":"2023012512325988800_B24","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/ng1929","article-title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","volume":"39","author":"Zilberman","year":"2007","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/12\/i163\/48875733\/bioinformatics_28_12_i163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/12\/i163\/48875733\/bioinformatics_28_12_i163.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,25]],"date-time":"2024-04-25T06:50:33Z","timestamp":1714027833000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/12\/i163\/269683"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,9]]},"references-count":24,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2012,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts231","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,6,15]]},"published":{"date-parts":[[2012,6,9]]}}}