Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1
Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correla...
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| description | Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correlated with the progression of AIDS. In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. Based on data from the microarray experiment, 4679 differentially methylated regions in the HIV positive subject with the significant peak values were identified. Selected genes were then validated in human T lymphocyte CEM*174 cell line and HIV/AIDS patients by comparing with normal subjects. We found that
IGFBP6
and
SATB2
were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS. |
| doi_str_mv | 10.1038/srep10806 |
| format | Article |
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IGFBP6
and
SATB2
were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep10806</identifier><identifier>PMID: 26039376</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/22 ; 45/61 ; 45/77 ; 631/250 ; 631/326/596 ; Acquired immune deficiency syndrome ; Adolescent ; AIDS ; Cell Line ; CpG Islands ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA microarrays ; Down-Regulation ; Epigenesis, Genetic ; Epigenomics ; Female ; Gene Expression Profiling ; Gene Expression Regulation ; Gene regulation ; Genome, Human ; Genomes ; HIV ; HIV Infections - genetics ; HIV Infections - virology ; HIV-1 - physiology ; Human immunodeficiency virus ; Humanities and Social Sciences ; Humans ; Immunoprecipitation ; Insulin-Like Growth Factor Binding Protein 6 - genetics ; Insulin-like growth factor-binding protein 6 ; Lymphocytes ; Matrix Attachment Region Binding Proteins - genetics ; multidisciplinary ; Promoter Regions, Genetic ; Promoters ; Reproducibility of Results ; Science ; T-Lymphocytes - metabolism ; T-Lymphocytes - virology ; Transcription Factors - genetics ; Twins ; Twins, Monozygotic ; Viral Load</subject><ispartof>Scientific reports, 2015-06, Vol.5 (1), p.10806-10806, Article 10806</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Jun 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited 2015 Macmillan Publishers Limited</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c438t-417703ca3a0c61dda41fa75256cc7b7df885cfed8eec9ba9099f81544e673a863</citedby><cites>FETCH-LOGICAL-c438t-417703ca3a0c61dda41fa75256cc7b7df885cfed8eec9ba9099f81544e673a863</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454074/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454074/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26039376$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Yinfeng</creatorcontrib><creatorcontrib>Li, Sai-Kam</creatorcontrib><creatorcontrib>Yi Yang, Kevin</creatorcontrib><creatorcontrib>Liu, Minghua</creatorcontrib><creatorcontrib>Lee, Nelson</creatorcontrib><creatorcontrib>Tang, Xian</creatorcontrib><creatorcontrib>Wang, Hui</creatorcontrib><creatorcontrib>Liu, Li</creatorcontrib><creatorcontrib>Chen, Zhiwei</creatorcontrib><creatorcontrib>Zhang, Chiyu</creatorcontrib><creatorcontrib>Wang, Jianhua</creatorcontrib><creatorcontrib>Kwok-Wing Tsui, Stephen</creatorcontrib><title>Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correlated with the progression of AIDS. In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. Based on data from the microarray experiment, 4679 differentially methylated regions in the HIV positive subject with the significant peak values were identified. Selected genes were then validated in human T lymphocyte CEM*174 cell line and HIV/AIDS patients by comparing with normal subjects. We found that
IGFBP6
and
SATB2
were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS.</description><subject>38/22</subject><subject>45/61</subject><subject>45/77</subject><subject>631/250</subject><subject>631/326/596</subject><subject>Acquired immune deficiency syndrome</subject><subject>Adolescent</subject><subject>AIDS</subject><subject>Cell Line</subject><subject>CpG Islands</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA microarrays</subject><subject>Down-Regulation</subject><subject>Epigenesis, Genetic</subject><subject>Epigenomics</subject><subject>Female</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation</subject><subject>Gene regulation</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>HIV</subject><subject>HIV Infections - genetics</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - physiology</subject><subject>Human immunodeficiency virus</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Immunoprecipitation</subject><subject>Insulin-Like Growth Factor Binding Protein 6 - genetics</subject><subject>Insulin-like growth factor-binding protein 6</subject><subject>Lymphocytes</subject><subject>Matrix Attachment Region Binding Proteins - genetics</subject><subject>multidisciplinary</subject><subject>Promoter Regions, Genetic</subject><subject>Promoters</subject><subject>Reproducibility of Results</subject><subject>Science</subject><subject>T-Lymphocytes - metabolism</subject><subject>T-Lymphocytes - virology</subject><subject>Transcription Factors - genetics</subject><subject>Twins</subject><subject>Twins, Monozygotic</subject><subject>Viral Load</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkV1rFDEUhoMotqy98A9IwBsVxuZ7khuhLf1YKFSw2suQzZzZnTKTrMlMy_57I7suq56bHHifvOckL0JvKflMCdenOcGaEk3UC3TMiJAV44y9POiP0EnOj6SUZEZQ8xodMUW44bU6Rg8Pq9gDXkKIA-ABxtWmd2MXA3YpuQ1O8ASuz3hcAW7ic6gSLKcdEVs8v746_6qwCw3-dnZ_zvBig2_mPyr6Br1qyz042Z0z9P3q8v7iprq9u55fnN1WXnA9VoLWNeHecUe8ok3jBG1dLZlU3teLumm1lr6FRgN4s3CGGNNqKoUAVXOnFZ-hL1vf9bQYoPEQxuR6u07d4NLGRtfZv5XQrewyPlkhpCC1KAYfdgYp_pwgj3bosoe-dwHilC1VWgkqWfnrGXr_D_oYpxTK8yzVxkglC1yoj1vKp5hLOO1-GUrs78TsPrHCvjvcfk_-yacAn7ZALlJYQjoY-Z_bL2wOnmM</recordid><startdate>20150603</startdate><enddate>20150603</enddate><creator>Zhang, Yinfeng</creator><creator>Li, Sai-Kam</creator><creator>Yi Yang, Kevin</creator><creator>Liu, Minghua</creator><creator>Lee, Nelson</creator><creator>Tang, Xian</creator><creator>Wang, Hui</creator><creator>Liu, Li</creator><creator>Chen, Zhiwei</creator><creator>Zhang, Chiyu</creator><creator>Wang, Jianhua</creator><creator>Kwok-Wing Tsui, Stephen</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><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>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150603</creationdate><title>Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1</title><author>Zhang, Yinfeng ; Li, Sai-Kam ; Yi Yang, Kevin ; Liu, Minghua ; Lee, Nelson ; Tang, Xian ; Wang, Hui ; Liu, Li ; Chen, Zhiwei ; Zhang, Chiyu ; Wang, Jianhua ; Kwok-Wing Tsui, Stephen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c438t-417703ca3a0c61dda41fa75256cc7b7df885cfed8eec9ba9099f81544e673a863</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>38/22</topic><topic>45/61</topic><topic>45/77</topic><topic>631/250</topic><topic>631/326/596</topic><topic>Acquired immune deficiency syndrome</topic><topic>Adolescent</topic><topic>AIDS</topic><topic>Cell Line</topic><topic>CpG Islands</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA microarrays</topic><topic>Down-Regulation</topic><topic>Epigenesis, Genetic</topic><topic>Epigenomics</topic><topic>Female</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation</topic><topic>Gene regulation</topic><topic>Genome, Human</topic><topic>Genomes</topic><topic>HIV</topic><topic>HIV Infections - genetics</topic><topic>HIV Infections - virology</topic><topic>HIV-1 - physiology</topic><topic>Human immunodeficiency virus</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Immunoprecipitation</topic><topic>Insulin-Like Growth Factor Binding Protein 6 - genetics</topic><topic>Insulin-like growth factor-binding protein 6</topic><topic>Lymphocytes</topic><topic>Matrix Attachment Region Binding Proteins - genetics</topic><topic>multidisciplinary</topic><topic>Promoter Regions, Genetic</topic><topic>Promoters</topic><topic>Reproducibility of Results</topic><topic>Science</topic><topic>T-Lymphocytes - metabolism</topic><topic>T-Lymphocytes - virology</topic><topic>Transcription Factors - genetics</topic><topic>Twins</topic><topic>Twins, Monozygotic</topic><topic>Viral Load</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Yinfeng</creatorcontrib><creatorcontrib>Li, Sai-Kam</creatorcontrib><creatorcontrib>Yi Yang, Kevin</creatorcontrib><creatorcontrib>Liu, Minghua</creatorcontrib><creatorcontrib>Lee, Nelson</creatorcontrib><creatorcontrib>Tang, Xian</creatorcontrib><creatorcontrib>Wang, Hui</creatorcontrib><creatorcontrib>Liu, Li</creatorcontrib><creatorcontrib>Chen, Zhiwei</creatorcontrib><creatorcontrib>Zhang, Chiyu</creatorcontrib><creatorcontrib>Wang, Jianhua</creatorcontrib><creatorcontrib>Kwok-Wing Tsui, Stephen</creatorcontrib><collection>Springer Nature OA Free Journals</collection><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>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech 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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Yinfeng</au><au>Li, Sai-Kam</au><au>Yi Yang, Kevin</au><au>Liu, Minghua</au><au>Lee, Nelson</au><au>Tang, Xian</au><au>Wang, Hui</au><au>Liu, Li</au><au>Chen, Zhiwei</au><au>Zhang, Chiyu</au><au>Wang, Jianhua</au><au>Kwok-Wing Tsui, Stephen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-06-03</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>10806</spage><epage>10806</epage><pages>10806-10806</pages><artnum>10806</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correlated with the progression of AIDS. In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation - microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. Based on data from the microarray experiment, 4679 differentially methylated regions in the HIV positive subject with the significant peak values were identified. Selected genes were then validated in human T lymphocyte CEM*174 cell line and HIV/AIDS patients by comparing with normal subjects. We found that
IGFBP6
and
SATB2
were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>26039376</pmid><doi>10.1038/srep10806</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 38/22 45/61 45/77 631/250 631/326/596 Acquired immune deficiency syndrome Adolescent AIDS Cell Line CpG Islands Deoxyribonucleic acid DNA DNA Methylation DNA microarrays Down-Regulation Epigenesis, Genetic Epigenomics Female Gene Expression Profiling Gene Expression Regulation Gene regulation Genome, Human Genomes HIV HIV Infections - genetics HIV Infections - virology HIV-1 - physiology Human immunodeficiency virus Humanities and Social Sciences Humans Immunoprecipitation Insulin-Like Growth Factor Binding Protein 6 - genetics Insulin-like growth factor-binding protein 6 Lymphocytes Matrix Attachment Region Binding Proteins - genetics multidisciplinary Promoter Regions, Genetic Promoters Reproducibility of Results Science T-Lymphocytes - metabolism T-Lymphocytes - virology Transcription Factors - genetics Twins Twins, Monozygotic Viral Load |
| title | Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1 |
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