Detecting DNA cytosine methylation using nanopore sequencing
A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment. In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, su...
Gespeichert in:
| Veröffentlicht in: | Nature methods 2017-04, Vol.14 (4), p.407-410 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 410 |
|---|---|
| container_issue | 4 |
| container_start_page | 407 |
| container_title | Nature methods |
| container_volume | 14 |
| creator | Simpson, Jared T Workman, Rachael E Zuzarte, P C David, Matei Dursi, L J Timp, Winston |
| description | A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation. |
| doi_str_mv | 10.1038/nmeth.4184 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1870642614</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2085797150</sourcerecordid><originalsourceid>FETCH-LOGICAL-c453t-9832d5e5dabbf6aca5c658ce4bb91807f457e1e946a868797fa30501150fc9023</originalsourceid><addsrcrecordid>eNptkN9LwzAQx4Mobk5f_AOk4IsonUmbtCn4MjZ_wdAXfQ5pdp0dbTKT9GH_vanbFMSnO-4-fO74InRO8JjglN_qFvzHmBJOD9CQMMrjnGB2uO9xQQboxLkVxmlKE3aMBglPCOcFH6K7GXhQvtbLaPYyidTGG1driHrlppG-NjrqXL_WUpu1sRA5-OxAqzA7RUeVbByc7eoIvT_cv02f4vnr4_N0Mo8VZamPC54mCwZsIcuyyqSSTGWMK6BlWRCO84qyHAgUNJM843mRVzLFDBPCcKUKnKQjdLX1rq0Jt50Xbe0UNI3UYDonCM9xRpOM0IBe_kFXprM6fCcSzFmQB2ugrreUssY5C5VY27qVdiMIFn2m4jtT0Wca4IudsitbWPyg-xADcLMFXFjpJdjfm__ovgAPyoA3</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2085797150</pqid></control><display><type>article</type><title>Detecting DNA cytosine methylation using nanopore sequencing</title><source>MEDLINE</source><source>Nature Journals Online</source><source>SpringerLink Journals - AutoHoldings</source><creator>Simpson, Jared T ; Workman, Rachael E ; Zuzarte, P C ; David, Matei ; Dursi, L J ; Timp, Winston</creator><creatorcontrib>Simpson, Jared T ; Workman, Rachael E ; Zuzarte, P C ; David, Matei ; Dursi, L J ; Timp, Winston</creatorcontrib><description>A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.</description><identifier>ISSN: 1548-7091</identifier><identifier>EISSN: 1548-7105</identifier><identifier>DOI: 10.1038/nmeth.4184</identifier><identifier>PMID: 28218898</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>45 ; 45/23 ; 5-Methylcytosine - analysis ; 631/114/794 ; 631/208/177 ; 631/208/514/1948 ; 631/61/350/1058 ; Bioinformatics ; Biological Microscopy ; Biological Techniques ; Biomedical Engineering/Biotechnology ; brief-communication ; Cell Line, Tumor ; CpG Islands ; Cytosine ; Cytosine - analysis ; Cytosine - metabolism ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA sequencing ; Escherichia coli - genetics ; Genome, Human ; Humans ; Life Sciences ; Markov Chains ; Nanopores ; Nucleotide sequence ; Porosity ; Proteomics</subject><ispartof>Nature methods, 2017-04, Vol.14 (4), p.407-410</ispartof><rights>Springer Nature America, Inc. 2017</rights><rights>Copyright Nature Publishing Group Apr 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c453t-9832d5e5dabbf6aca5c658ce4bb91807f457e1e946a868797fa30501150fc9023</citedby><cites>FETCH-LOGICAL-c453t-9832d5e5dabbf6aca5c658ce4bb91807f457e1e946a868797fa30501150fc9023</cites><orcidid>0000-0002-4697-798X ; 0000-0003-2083-6027</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nmeth.4184$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nmeth.4184$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28218898$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Simpson, Jared T</creatorcontrib><creatorcontrib>Workman, Rachael E</creatorcontrib><creatorcontrib>Zuzarte, P C</creatorcontrib><creatorcontrib>David, Matei</creatorcontrib><creatorcontrib>Dursi, L J</creatorcontrib><creatorcontrib>Timp, Winston</creatorcontrib><title>Detecting DNA cytosine methylation using nanopore sequencing</title><title>Nature methods</title><addtitle>Nat Methods</addtitle><addtitle>Nat Methods</addtitle><description>A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.</description><subject>45</subject><subject>45/23</subject><subject>5-Methylcytosine - analysis</subject><subject>631/114/794</subject><subject>631/208/177</subject><subject>631/208/514/1948</subject><subject>631/61/350/1058</subject><subject>Bioinformatics</subject><subject>Biological Microscopy</subject><subject>Biological Techniques</subject><subject>Biomedical Engineering/Biotechnology</subject><subject>brief-communication</subject><subject>Cell Line, Tumor</subject><subject>CpG Islands</subject><subject>Cytosine</subject><subject>Cytosine - analysis</subject><subject>Cytosine - metabolism</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA sequencing</subject><subject>Escherichia coli - genetics</subject><subject>Genome, Human</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Markov Chains</subject><subject>Nanopores</subject><subject>Nucleotide sequence</subject><subject>Porosity</subject><subject>Proteomics</subject><issn>1548-7091</issn><issn>1548-7105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNptkN9LwzAQx4Mobk5f_AOk4IsonUmbtCn4MjZ_wdAXfQ5pdp0dbTKT9GH_vanbFMSnO-4-fO74InRO8JjglN_qFvzHmBJOD9CQMMrjnGB2uO9xQQboxLkVxmlKE3aMBglPCOcFH6K7GXhQvtbLaPYyidTGG1driHrlppG-NjrqXL_WUpu1sRA5-OxAqzA7RUeVbByc7eoIvT_cv02f4vnr4_N0Mo8VZamPC54mCwZsIcuyyqSSTGWMK6BlWRCO84qyHAgUNJM843mRVzLFDBPCcKUKnKQjdLX1rq0Jt50Xbe0UNI3UYDonCM9xRpOM0IBe_kFXprM6fCcSzFmQB2ugrreUssY5C5VY27qVdiMIFn2m4jtT0Wca4IudsitbWPyg-xADcLMFXFjpJdjfm__ovgAPyoA3</recordid><startdate>20170401</startdate><enddate>20170401</enddate><creator>Simpson, Jared T</creator><creator>Workman, Rachael E</creator><creator>Zuzarte, P C</creator><creator>David, Matei</creator><creator>Dursi, L J</creator><creator>Timp, Winston</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7SS</scope><scope>7TK</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4697-798X</orcidid><orcidid>https://orcid.org/0000-0003-2083-6027</orcidid></search><sort><creationdate>20170401</creationdate><title>Detecting DNA cytosine methylation using nanopore sequencing</title><author>Simpson, Jared T ; Workman, Rachael E ; Zuzarte, P C ; David, Matei ; Dursi, L J ; Timp, Winston</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c453t-9832d5e5dabbf6aca5c658ce4bb91807f457e1e946a868797fa30501150fc9023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>45</topic><topic>45/23</topic><topic>5-Methylcytosine - analysis</topic><topic>631/114/794</topic><topic>631/208/177</topic><topic>631/208/514/1948</topic><topic>631/61/350/1058</topic><topic>Bioinformatics</topic><topic>Biological Microscopy</topic><topic>Biological Techniques</topic><topic>Biomedical Engineering/Biotechnology</topic><topic>brief-communication</topic><topic>Cell Line, Tumor</topic><topic>CpG Islands</topic><topic>Cytosine</topic><topic>Cytosine - analysis</topic><topic>Cytosine - metabolism</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA sequencing</topic><topic>Escherichia coli - genetics</topic><topic>Genome, Human</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Markov Chains</topic><topic>Nanopores</topic><topic>Nucleotide sequence</topic><topic>Porosity</topic><topic>Proteomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Simpson, Jared T</creatorcontrib><creatorcontrib>Workman, Rachael E</creatorcontrib><creatorcontrib>Zuzarte, P C</creatorcontrib><creatorcontrib>David, Matei</creatorcontrib><creatorcontrib>Dursi, L J</creatorcontrib><creatorcontrib>Timp, Winston</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Nature methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Simpson, Jared T</au><au>Workman, Rachael E</au><au>Zuzarte, P C</au><au>David, Matei</au><au>Dursi, L J</au><au>Timp, Winston</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detecting DNA cytosine methylation using nanopore sequencing</atitle><jtitle>Nature methods</jtitle><stitle>Nat Methods</stitle><addtitle>Nat Methods</addtitle><date>2017-04-01</date><risdate>2017</risdate><volume>14</volume><issue>4</issue><spage>407</spage><epage>410</epage><pages>407-410</pages><issn>1548-7091</issn><eissn>1548-7105</eissn><abstract>A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>28218898</pmid><doi>10.1038/nmeth.4184</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0002-4697-798X</orcidid><orcidid>https://orcid.org/0000-0003-2083-6027</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1548-7091 |
| ispartof | Nature methods, 2017-04, Vol.14 (4), p.407-410 |
| issn | 1548-7091 1548-7105 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1870642614 |
| source | MEDLINE; Nature Journals Online; SpringerLink Journals - AutoHoldings |
| subjects | 45 45/23 5-Methylcytosine - analysis 631/114/794 631/208/177 631/208/514/1948 631/61/350/1058 Bioinformatics Biological Microscopy Biological Techniques Biomedical Engineering/Biotechnology brief-communication Cell Line, Tumor CpG Islands Cytosine Cytosine - analysis Cytosine - metabolism Deoxyribonucleic acid DNA DNA Methylation DNA sequencing Escherichia coli - genetics Genome, Human Humans Life Sciences Markov Chains Nanopores Nucleotide sequence Porosity Proteomics |
| title | Detecting DNA cytosine methylation using nanopore sequencing |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-06T16%3A37%3A16IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Detecting%20DNA%20cytosine%20methylation%20using%20nanopore%20sequencing&rft.jtitle=Nature%20methods&rft.au=Simpson,%20Jared%20T&rft.date=2017-04-01&rft.volume=14&rft.issue=4&rft.spage=407&rft.epage=410&rft.pages=407-410&rft.issn=1548-7091&rft.eissn=1548-7105&rft_id=info:doi/10.1038/nmeth.4184&rft_dat=%3Cproquest_cross%3E2085797150%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2085797150&rft_id=info:pmid/28218898&rfr_iscdi=true |