Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily
Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) located near or within genes might affect their expression. We used the KIAA1245/NBPF human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes...
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| Veröffentlicht in: | Genetica 2011-06, Vol.139 (6), p.733-741 |
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| creator | Abrarova, Natalia Simonova, Larisa Vinogradova, Tatyana Sverdlov, Eugene |
| description | Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) located near or within genes might affect their expression. We used the
KIAA1245/NBPF
human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes: three of them contain an LTR in the second intron, and two genes lack it. Earlier we reported that the second and third exons of only LTR-containing genes of this subfamily could be detected in mature mRNAs of various cell lines and human tissues. The corresponding parts of mRNA of LTR-lacking genes analyzed in our study were absent from EST libraries, but other fragments of their mRNAs were available in EST databases. For a more unbiased view on the correlation between gene transcription and the intronic LTRs, in the present work we analyzed non-spliced pre-mRNA thus avoiding splicing effects. Based on RT–PCR analysis, we demonstrated that the
KIAA1245/NBPF
LTR-lacking gene
AL592309/NBPF3
was transcriptionally active, but the LTR-containing genes showed significantly higher transcription levels. The data are in agreement with the suggestion that HERV-K LTRs within the second intron of the
KIAA1245/NBPF
subfamily genes might affect their transcriptional activity. However, it still remains to be investigated whether the revealed effect is due just to the LTR insertion or other factors are responsible for the difference. |
| doi_str_mv | 10.1007/s10709-011-9577-x |
| format | Article |
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KIAA1245/NBPF
human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes: three of them contain an LTR in the second intron, and two genes lack it. Earlier we reported that the second and third exons of only LTR-containing genes of this subfamily could be detected in mature mRNAs of various cell lines and human tissues. The corresponding parts of mRNA of LTR-lacking genes analyzed in our study were absent from EST libraries, but other fragments of their mRNAs were available in EST databases. For a more unbiased view on the correlation between gene transcription and the intronic LTRs, in the present work we analyzed non-spliced pre-mRNA thus avoiding splicing effects. Based on RT–PCR analysis, we demonstrated that the
KIAA1245/NBPF
LTR-lacking gene
AL592309/NBPF3
was transcriptionally active, but the LTR-containing genes showed significantly higher transcription levels. The data are in agreement with the suggestion that HERV-K LTRs within the second intron of the
KIAA1245/NBPF
subfamily genes might affect their transcriptional activity. However, it still remains to be investigated whether the revealed effect is due just to the LTR insertion or other factors are responsible for the difference.</description><identifier>ISSN: 0016-6707</identifier><identifier>EISSN: 1573-6857</identifier><identifier>DOI: 10.1007/s10709-011-9577-x</identifier><identifier>PMID: 21544646</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Genetics and Genomics ; Base Sequence ; Biomedical and Life Sciences ; Cell Line, Tumor ; Data processing ; Endogenous Retroviruses - genetics ; Endogenous Retroviruses - metabolism ; Evolutionary Biology ; Gene Expression Regulation, Viral ; Gene Order ; HEK293 Cells ; HeLa Cells ; Human Genetics ; Humans ; Jurkat Cells ; Life Sciences ; Microbial Genetics and Genomics ; Plant Genetics and Genomics ; Retrovirus ; RNA Precursors - genetics ; RNA Splice Sites - genetics ; Sequence Alignment ; Terminal Repeat Sequences - genetics</subject><ispartof>Genetica, 2011-06, Vol.139 (6), p.733-741</ispartof><rights>Springer Science+Business Media B.V. 2011</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c402t-c3ecd40fc871929103b69e65669686ec0a224f1c953191d3317e1cd18fcea9f53</citedby><cites>FETCH-LOGICAL-c402t-c3ecd40fc871929103b69e65669686ec0a224f1c953191d3317e1cd18fcea9f53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10709-011-9577-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10709-011-9577-x$$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/21544646$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Abrarova, Natalia</creatorcontrib><creatorcontrib>Simonova, Larisa</creatorcontrib><creatorcontrib>Vinogradova, Tatyana</creatorcontrib><creatorcontrib>Sverdlov, Eugene</creatorcontrib><title>Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily</title><title>Genetica</title><addtitle>Genetica</addtitle><addtitle>Genetica</addtitle><description>Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) located near or within genes might affect their expression. We used the
KIAA1245/NBPF
human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes: three of them contain an LTR in the second intron, and two genes lack it. Earlier we reported that the second and third exons of only LTR-containing genes of this subfamily could be detected in mature mRNAs of various cell lines and human tissues. The corresponding parts of mRNA of LTR-lacking genes analyzed in our study were absent from EST libraries, but other fragments of their mRNAs were available in EST databases. For a more unbiased view on the correlation between gene transcription and the intronic LTRs, in the present work we analyzed non-spliced pre-mRNA thus avoiding splicing effects. Based on RT–PCR analysis, we demonstrated that the
KIAA1245/NBPF
LTR-lacking gene
AL592309/NBPF3
was transcriptionally active, but the LTR-containing genes showed significantly higher transcription levels. The data are in agreement with the suggestion that HERV-K LTRs within the second intron of the
KIAA1245/NBPF
subfamily genes might affect their transcriptional activity. However, it still remains to be investigated whether the revealed effect is due just to the LTR insertion or other factors are responsible for the difference.</description><subject>Animal Genetics and Genomics</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Cell Line, Tumor</subject><subject>Data processing</subject><subject>Endogenous Retroviruses - genetics</subject><subject>Endogenous Retroviruses - metabolism</subject><subject>Evolutionary Biology</subject><subject>Gene Expression Regulation, Viral</subject><subject>Gene Order</subject><subject>HEK293 Cells</subject><subject>HeLa Cells</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Jurkat Cells</subject><subject>Life Sciences</subject><subject>Microbial Genetics and Genomics</subject><subject>Plant Genetics and Genomics</subject><subject>Retrovirus</subject><subject>RNA Precursors - genetics</subject><subject>RNA Splice Sites - genetics</subject><subject>Sequence Alignment</subject><subject>Terminal Repeat Sequences - 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genetics</topic><topic>Endogenous Retroviruses - metabolism</topic><topic>Evolutionary Biology</topic><topic>Gene Expression Regulation, Viral</topic><topic>Gene Order</topic><topic>HEK293 Cells</topic><topic>HeLa Cells</topic><topic>Human Genetics</topic><topic>Humans</topic><topic>Jurkat Cells</topic><topic>Life Sciences</topic><topic>Microbial Genetics and Genomics</topic><topic>Plant Genetics and Genomics</topic><topic>Retrovirus</topic><topic>RNA Precursors - genetics</topic><topic>RNA Splice Sites - genetics</topic><topic>Sequence Alignment</topic><topic>Terminal Repeat Sequences - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Abrarova, Natalia</creatorcontrib><creatorcontrib>Simonova, Larisa</creatorcontrib><creatorcontrib>Vinogradova, Tatyana</creatorcontrib><creatorcontrib>Sverdlov, Eugene</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>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</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>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>AIDS and Cancer Research Abstracts</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>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genetica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Abrarova, Natalia</au><au>Simonova, Larisa</au><au>Vinogradova, Tatyana</au><au>Sverdlov, Eugene</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily</atitle><jtitle>Genetica</jtitle><stitle>Genetica</stitle><addtitle>Genetica</addtitle><date>2011-06-01</date><risdate>2011</risdate><volume>139</volume><issue>6</issue><spage>733</spage><epage>741</epage><pages>733-741</pages><issn>0016-6707</issn><eissn>1573-6857</eissn><abstract>Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) located near or within genes might affect their expression. We used the
KIAA1245/NBPF
human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes: three of them contain an LTR in the second intron, and two genes lack it. Earlier we reported that the second and third exons of only LTR-containing genes of this subfamily could be detected in mature mRNAs of various cell lines and human tissues. The corresponding parts of mRNA of LTR-lacking genes analyzed in our study were absent from EST libraries, but other fragments of their mRNAs were available in EST databases. For a more unbiased view on the correlation between gene transcription and the intronic LTRs, in the present work we analyzed non-spliced pre-mRNA thus avoiding splicing effects. Based on RT–PCR analysis, we demonstrated that the
KIAA1245/NBPF
LTR-lacking gene
AL592309/NBPF3
was transcriptionally active, but the LTR-containing genes showed significantly higher transcription levels. The data are in agreement with the suggestion that HERV-K LTRs within the second intron of the
KIAA1245/NBPF
subfamily genes might affect their transcriptional activity. However, it still remains to be investigated whether the revealed effect is due just to the LTR insertion or other factors are responsible for the difference.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>21544646</pmid><doi>10.1007/s10709-011-9577-x</doi><tpages>9</tpages></addata></record> |
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| ispartof | Genetica, 2011-06, Vol.139 (6), p.733-741 |
| issn | 0016-6707 1573-6857 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals |
| subjects | Animal Genetics and Genomics Base Sequence Biomedical and Life Sciences Cell Line, Tumor Data processing Endogenous Retroviruses - genetics Endogenous Retroviruses - metabolism Evolutionary Biology Gene Expression Regulation, Viral Gene Order HEK293 Cells HeLa Cells Human Genetics Humans Jurkat Cells Life Sciences Microbial Genetics and Genomics Plant Genetics and Genomics Retrovirus RNA Precursors - genetics RNA Splice Sites - genetics Sequence Alignment Terminal Repeat Sequences - genetics |
| title | Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily |
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