Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells
The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs. In this study,...
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| Veröffentlicht in: | BMC genomics 2016-11, Vol.17 (1), p.908-908, Article 908 |
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| description | The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs.
In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5' end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.
The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs. |
| doi_str_mv | 10.1186/s12864-016-3252-7 |
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In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5' end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.
The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-016-3252-7</identifier><identifier>PMID: 27835943</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Endothelial Growth Factors - genetics ; Experiments ; Genes ; Genetic transcription ; HCT116 Cells ; Humans ; Libraries ; MicroRNA ; MicroRNAs ; MicroRNAs - chemistry ; MicroRNAs - genetics ; MicroRNAs - metabolism ; Observations ; Promoter Regions, Genetic ; Promoters (Genetics) ; Properties ; Protein Binding ; Proteins ; Ribonuclease III - deficiency ; Ribonuclease III - genetics ; Rodents ; Sequence Analysis, RNA ; Studies ; Transcription factors ; Transcription Factors - metabolism ; Transcription Initiation Site ; Transcription, Genetic</subject><ispartof>BMC genomics, 2016-11, Vol.17 (1), p.908-908, Article 908</ispartof><rights>COPYRIGHT 2016 BioMed Central Ltd.</rights><rights>Copyright BioMed Central 2016</rights><rights>The Author(s). 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-a342a56b0b0b57fc1f94954fa640b06409bcc95fe9bb21768632feb4b9b642e93</citedby><cites>FETCH-LOGICAL-c528t-a342a56b0b0b57fc1f94954fa640b06409bcc95fe9bb21768632feb4b9b642e93</cites><orcidid>0000-0001-6434-2235</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106785/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106785/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27835943$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jeong, Geon</creatorcontrib><creatorcontrib>Lim, Yeong-Hwan</creatorcontrib><creatorcontrib>Kim, Young-Kook</creatorcontrib><title>Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs.
In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5' end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.
The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.</description><subject>Endothelial Growth Factors - genetics</subject><subject>Experiments</subject><subject>Genes</subject><subject>Genetic transcription</subject><subject>HCT116 Cells</subject><subject>Humans</subject><subject>Libraries</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - chemistry</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>Observations</subject><subject>Promoter Regions, Genetic</subject><subject>Promoters (Genetics)</subject><subject>Properties</subject><subject>Protein Binding</subject><subject>Proteins</subject><subject>Ribonuclease III - deficiency</subject><subject>Ribonuclease III - genetics</subject><subject>Rodents</subject><subject>Sequence Analysis, RNA</subject><subject>Studies</subject><subject>Transcription factors</subject><subject>Transcription Factors - metabolism</subject><subject>Transcription Initiation Site</subject><subject>Transcription, Genetic</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptkl1vFSEQhjdGY2v1B3hjSLzRi607LLBwY3JSP9qkseZUrwlL4RzaXdgCa_Tfy-bU2mPMJECG5x0yw1tVL6E5BuDsXQLMGakbYHWLKa67R9UhkA5qDIw8fnA-qJ6ldN000HFMn1YHuOMtFaQ9rOTXaLRLBo1qmpzfoGBR3hqUo_JJRzdlFzxKWcWMkssmLcB2HpVHo9MxrL-sEprTovywvrg8XaEbH_RNmDPSZhjS8-qJVUMyL-72o-r7p4_fTk7r84vPZyer81pTzHOtWoIVZX1TgnZWgxVEUGIVIyVVFtFrLag1ou8xdIyzFlvTk170jGAj2qPq_a7uNPejudLGlw4GOUU3qvhLBuXk_o13W7kJPySFhnWclgJv7grEcDublOXo0tKC8ibMSQJvBWBoMSno63_Q6zBHX9orFKFYEAriL7VRg5HO21De1UtRuSJMcAas4YU6_g9V4sqU-QZvrCv5PcHbPUFhsvmZN2pOSZ5drvdZ2LHlo1KKxt7PAxq5OEjuHCSLg-TiINkVzauHg7xX_LFM-xvJFr-N</recordid><startdate>20161111</startdate><enddate>20161111</enddate><creator>Jeong, Geon</creator><creator>Lim, Yeong-Hwan</creator><creator>Kim, Young-Kook</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</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>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</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>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-6434-2235</orcidid></search><sort><creationdate>20161111</creationdate><title>Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells</title><author>Jeong, Geon ; Lim, Yeong-Hwan ; Kim, Young-Kook</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-a342a56b0b0b57fc1f94954fa640b06409bcc95fe9bb21768632feb4b9b642e93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Endothelial Growth Factors - genetics</topic><topic>Experiments</topic><topic>Genes</topic><topic>Genetic transcription</topic><topic>HCT116 Cells</topic><topic>Humans</topic><topic>Libraries</topic><topic>MicroRNA</topic><topic>MicroRNAs</topic><topic>MicroRNAs - chemistry</topic><topic>MicroRNAs - genetics</topic><topic>MicroRNAs - metabolism</topic><topic>Observations</topic><topic>Promoter Regions, Genetic</topic><topic>Promoters (Genetics)</topic><topic>Properties</topic><topic>Protein Binding</topic><topic>Proteins</topic><topic>Ribonuclease III - deficiency</topic><topic>Ribonuclease III - genetics</topic><topic>Rodents</topic><topic>Sequence Analysis, RNA</topic><topic>Studies</topic><topic>Transcription factors</topic><topic>Transcription Factors - metabolism</topic><topic>Transcription Initiation Site</topic><topic>Transcription, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jeong, Geon</creatorcontrib><creatorcontrib>Lim, Yeong-Hwan</creatorcontrib><creatorcontrib>Kim, Young-Kook</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</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>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</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>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>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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 China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jeong, Geon</au><au>Lim, Yeong-Hwan</au><au>Kim, Young-Kook</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2016-11-11</date><risdate>2016</risdate><volume>17</volume><issue>1</issue><spage>908</spage><epage>908</epage><pages>908-908</pages><artnum>908</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>The expression of microRNAs (miRNAs) is primarily regulated during their transcription. However, the transcriptional regulation of miRNA genes has not been studied extensively owing to the lack of sufficient information about the promoters and transcription start sites of most miRNAs.
In this study, we identified the transcription start sites of human primary miRNAs (pri-miRNAs) using DROSHA knockout cells. DROSHA knockout resulted in increased accumulation of pri-miRNAs and facilitated the precise mapping of their 5' end nucleotides using the rapid amplification of cDNA ends (RACE) technique. By analyzing the promoter region encompassing the transcription start sites of miRNAs, we found that the unrelated miRNAs in their sequences have many common elements in their promoters for binding the same transcription factors. Moreover, by analyzing intronic miRNAs, we also obtained comprehensive evidence that miRNA-harboring introns are spliced more slowly than other introns.
The precisely mapped transcription start sites of pri-miRNAs, and the list of transcription factors for pri-miRNAs regulation, will be valuable resources for future studies to understand the regulatory network of miRNAs.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>27835943</pmid><doi>10.1186/s12864-016-3252-7</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0001-6434-2235</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central Open Access; Springer Nature OA Free Journals; Springer Nature - Complete Springer Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Endothelial Growth Factors - genetics Experiments Genes Genetic transcription HCT116 Cells Humans Libraries MicroRNA MicroRNAs MicroRNAs - chemistry MicroRNAs - genetics MicroRNAs - metabolism Observations Promoter Regions, Genetic Promoters (Genetics) Properties Protein Binding Proteins Ribonuclease III - deficiency Ribonuclease III - genetics Rodents Sequence Analysis, RNA Studies Transcription factors Transcription Factors - metabolism Transcription Initiation Site Transcription, Genetic |
| title | Precise mapping of the transcription start sites of human microRNAs using DROSHA knockout cells |
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