Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes
Neuropeptide Y (NPY) is a potent orexigenic agent. The molecular mechanisms underlying the regulation of bovine NPY gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine NPY gene, (ii) investig...
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| Veröffentlicht in: | Molecular biology reports 2012-02, Vol.39 (2), p.919-928 |
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| creator | Alam, Tanweer Bahar, Bojlul Waters, Sinéad M. McGee, Mark O’Doherty, John V. Sweeney, Torres |
| description | Neuropeptide Y (NPY) is a potent orexigenic agent. The molecular mechanisms underlying the regulation of bovine
NPY
gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine
NPY
gene, (ii) investigate the effects of these SNPs by measuring promoter transcriptional activities of different bovine
NPY
promoter haplotypes and; (iii) identify the minimal promoter region (MPR) required for basal activity of the
NPY
gene in vitro. Seventeen SNPs were identified in the promoter region. Of these, 14 affected putative transcription factors binding motifs including a TATA binding protein factor at −20, GC-Box factors SP1 at −170 and GATA binding motifs at −120 and −347. The SNPs were assigned to five major haplotypes (BtNPY_H1-5), of which BtNPY_H5 had maximum transcriptional activity. The region extending to −134 nt was identified as the MPR. This MPR was confirmed by the identification of a putative TATA box (−29 nt) and two SP1/GC binding sites (−94 and −118 nt), within this region. However, promoter expression was significantly enhanced when the construct contained the −614 to −1019 nt region. In conclusion, a number of SNPs characterised in the bovine
NPY
promoter especially those affecting the transcription factor binding sites, enhancer and repressor regions have the potential to affect
NPY
gene expression. Natural variation exists in the promoter region of the bovine
NPY
gene, which should be further explored for selection of energetic efficiency in cattle. |
| doi_str_mv | 10.1007/s11033-011-0817-z |
| format | Article |
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NPY
gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine
NPY
gene, (ii) investigate the effects of these SNPs by measuring promoter transcriptional activities of different bovine
NPY
promoter haplotypes and; (iii) identify the minimal promoter region (MPR) required for basal activity of the
NPY
gene in vitro. Seventeen SNPs were identified in the promoter region. Of these, 14 affected putative transcription factors binding motifs including a TATA binding protein factor at −20, GC-Box factors SP1 at −170 and GATA binding motifs at −120 and −347. The SNPs were assigned to five major haplotypes (BtNPY_H1-5), of which BtNPY_H5 had maximum transcriptional activity. The region extending to −134 nt was identified as the MPR. This MPR was confirmed by the identification of a putative TATA box (−29 nt) and two SP1/GC binding sites (−94 and −118 nt), within this region. However, promoter expression was significantly enhanced when the construct contained the −614 to −1019 nt region. In conclusion, a number of SNPs characterised in the bovine
NPY
promoter especially those affecting the transcription factor binding sites, enhancer and repressor regions have the potential to affect
NPY
gene expression. Natural variation exists in the promoter region of the bovine
NPY
gene, which should be further explored for selection of energetic efficiency in cattle.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-011-0817-z</identifier><identifier>PMID: 21562764</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Animals ; Base Sequence ; Biomedical and Life Sciences ; Cattle - genetics ; DNA Primers - genetics ; Enhancers ; Gene expression ; Gene Expression Regulation - genetics ; Genetic Variation ; Guanylate cyclase ; Haplotypes ; Haplotypes - genetics ; Histology ; Life Sciences ; Linear Models ; Linkage Disequilibrium ; Molecular biology ; Molecular modelling ; Molecular Sequence Data ; Morphology ; Neuropeptide Y ; Neuropeptide Y - genetics ; Neuropeptide Y - metabolism ; Peptides ; Polymerase Chain Reaction ; Polymorphism ; Polymorphism, Single Nucleotide - genetics ; Promoter Regions, Genetic - genetics ; Promoters ; Protein Interaction Domains and Motifs - genetics ; Repressors ; Sequence Analysis, DNA ; Single-nucleotide polymorphism ; Sp1 protein ; Tata box ; TATA-binding protein ; Transcription factors</subject><ispartof>Molecular biology reports, 2012-02, Vol.39 (2), p.919-928</ispartof><rights>Springer Science+Business Media B.V. 2011</rights><rights>Springer Science+Business Media B.V. 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c403t-c1d9d124c1c9ecf6244f60621f7c88d90d4be1a99ecd0acf9d5cc81ed62ad3e03</citedby><cites>FETCH-LOGICAL-c403t-c1d9d124c1c9ecf6244f60621f7c88d90d4be1a99ecd0acf9d5cc81ed62ad3e03</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/s11033-011-0817-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-011-0817-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21562764$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alam, Tanweer</creatorcontrib><creatorcontrib>Bahar, Bojlul</creatorcontrib><creatorcontrib>Waters, Sinéad M.</creatorcontrib><creatorcontrib>McGee, Mark</creatorcontrib><creatorcontrib>O’Doherty, John V.</creatorcontrib><creatorcontrib>Sweeney, Torres</creatorcontrib><title>Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Neuropeptide Y (NPY) is a potent orexigenic agent. The molecular mechanisms underlying the regulation of bovine
NPY
gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine
NPY
gene, (ii) investigate the effects of these SNPs by measuring promoter transcriptional activities of different bovine
NPY
promoter haplotypes and; (iii) identify the minimal promoter region (MPR) required for basal activity of the
NPY
gene in vitro. Seventeen SNPs were identified in the promoter region. Of these, 14 affected putative transcription factors binding motifs including a TATA binding protein factor at −20, GC-Box factors SP1 at −170 and GATA binding motifs at −120 and −347. The SNPs were assigned to five major haplotypes (BtNPY_H1-5), of which BtNPY_H5 had maximum transcriptional activity. The region extending to −134 nt was identified as the MPR. This MPR was confirmed by the identification of a putative TATA box (−29 nt) and two SP1/GC binding sites (−94 and −118 nt), within this region. However, promoter expression was significantly enhanced when the construct contained the −614 to −1019 nt region. In conclusion, a number of SNPs characterised in the bovine
NPY
promoter especially those affecting the transcription factor binding sites, enhancer and repressor regions have the potential to affect
NPY
gene expression. Natural variation exists in the promoter region of the bovine
NPY
gene, which should be further explored for selection of energetic efficiency in cattle.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Cattle - genetics</subject><subject>DNA Primers - genetics</subject><subject>Enhancers</subject><subject>Gene expression</subject><subject>Gene Expression Regulation - genetics</subject><subject>Genetic Variation</subject><subject>Guanylate cyclase</subject><subject>Haplotypes</subject><subject>Haplotypes - genetics</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Linear Models</subject><subject>Linkage Disequilibrium</subject><subject>Molecular biology</subject><subject>Molecular modelling</subject><subject>Molecular Sequence Data</subject><subject>Morphology</subject><subject>Neuropeptide Y</subject><subject>Neuropeptide Y - genetics</subject><subject>Neuropeptide Y - metabolism</subject><subject>Peptides</subject><subject>Polymerase Chain Reaction</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Promoters</subject><subject>Protein Interaction Domains and Motifs - genetics</subject><subject>Repressors</subject><subject>Sequence Analysis, DNA</subject><subject>Single-nucleotide polymorphism</subject><subject>Sp1 protein</subject><subject>Tata box</subject><subject>TATA-binding protein</subject><subject>Transcription factors</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</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>eNp9kcFu1DAQhi0EotvCA3BBFhe4BGZsJ3aOqGoBqRIXOHCKvPak6yobBztZqX2IPjNedikCCU6Wxt__ja2fsRcIbxFAv8uIIGUFiBUY1NXdI7bCWstKtdo8ZiuQgJUyNZ6w05xvAEChrp-yE4F1I3SjVuz-chndHOJoB-42Nlk3UwrZ7kc89nzeEF_HXRiJj7SkONE0B0_8G7-mMptS3MaS4Hb0nHZ2WP5IzsmO2aUwHTcUe9iFOVDeEw_hjZ2GON9OlJ-xJ70dMj0_nmfs6-XFl_OP1dXnD5_O319VToGcK4e-9SiUQ9eS6xuhVN9AI7DXzhjfgldrQtuWSw_W9a2vnTNIvhHWSwJ5xl4fvOUN3xfKc7cN2dEw2JHikrsWpRaiNqKQb_5LIggDQoBWBX31F3oTl1T-_dMnBRo0BcID5FLMOVHfTSlsbbotpm7fandotSutdvtWu7uSeXkUL-st-YfErxoLIA5ALlfjNaXfm_9t_QFwabF2</recordid><startdate>20120201</startdate><enddate>20120201</enddate><creator>Alam, Tanweer</creator><creator>Bahar, Bojlul</creator><creator>Waters, Sinéad M.</creator><creator>McGee, Mark</creator><creator>O’Doherty, John V.</creator><creator>Sweeney, Torres</creator><general>Springer Netherlands</general><general>Springer Nature B.V</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>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</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>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</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>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20120201</creationdate><title>Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes</title><author>Alam, Tanweer ; Bahar, Bojlul ; Waters, Sinéad M. ; McGee, Mark ; O’Doherty, John V. ; Sweeney, Torres</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-c1d9d124c1c9ecf6244f60621f7c88d90d4be1a99ecd0acf9d5cc81ed62ad3e03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>Biomedical and Life Sciences</topic><topic>Cattle - genetics</topic><topic>DNA Primers - genetics</topic><topic>Enhancers</topic><topic>Gene expression</topic><topic>Gene Expression Regulation - genetics</topic><topic>Genetic Variation</topic><topic>Guanylate cyclase</topic><topic>Haplotypes</topic><topic>Haplotypes - genetics</topic><topic>Histology</topic><topic>Life Sciences</topic><topic>Linear Models</topic><topic>Linkage Disequilibrium</topic><topic>Molecular biology</topic><topic>Molecular modelling</topic><topic>Molecular Sequence Data</topic><topic>Morphology</topic><topic>Neuropeptide Y</topic><topic>Neuropeptide Y - genetics</topic><topic>Neuropeptide Y - metabolism</topic><topic>Peptides</topic><topic>Polymerase Chain Reaction</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Promoter Regions, Genetic - genetics</topic><topic>Promoters</topic><topic>Protein Interaction Domains and Motifs - genetics</topic><topic>Repressors</topic><topic>Sequence Analysis, DNA</topic><topic>Single-nucleotide polymorphism</topic><topic>Sp1 protein</topic><topic>Tata box</topic><topic>TATA-binding protein</topic><topic>Transcription factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alam, Tanweer</creatorcontrib><creatorcontrib>Bahar, Bojlul</creatorcontrib><creatorcontrib>Waters, Sinéad M.</creatorcontrib><creatorcontrib>McGee, Mark</creatorcontrib><creatorcontrib>O’Doherty, John V.</creatorcontrib><creatorcontrib>Sweeney, Torres</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>Neurosciences Abstracts</collection><collection>Nucleic Acids 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>Science 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 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>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>Science Database</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>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alam, Tanweer</au><au>Bahar, Bojlul</au><au>Waters, Sinéad M.</au><au>McGee, Mark</au><au>O’Doherty, John V.</au><au>Sweeney, Torres</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2012-02-01</date><risdate>2012</risdate><volume>39</volume><issue>2</issue><spage>919</spage><epage>928</epage><pages>919-928</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Neuropeptide Y (NPY) is a potent orexigenic agent. The molecular mechanisms underlying the regulation of bovine
NPY
gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine
NPY
gene, (ii) investigate the effects of these SNPs by measuring promoter transcriptional activities of different bovine
NPY
promoter haplotypes and; (iii) identify the minimal promoter region (MPR) required for basal activity of the
NPY
gene in vitro. Seventeen SNPs were identified in the promoter region. Of these, 14 affected putative transcription factors binding motifs including a TATA binding protein factor at −20, GC-Box factors SP1 at −170 and GATA binding motifs at −120 and −347. The SNPs were assigned to five major haplotypes (BtNPY_H1-5), of which BtNPY_H5 had maximum transcriptional activity. The region extending to −134 nt was identified as the MPR. This MPR was confirmed by the identification of a putative TATA box (−29 nt) and two SP1/GC binding sites (−94 and −118 nt), within this region. However, promoter expression was significantly enhanced when the construct contained the −614 to −1019 nt region. In conclusion, a number of SNPs characterised in the bovine
NPY
promoter especially those affecting the transcription factor binding sites, enhancer and repressor regions have the potential to affect
NPY
gene expression. Natural variation exists in the promoter region of the bovine
NPY
gene, which should be further explored for selection of energetic efficiency in cattle.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>21562764</pmid><doi>10.1007/s11033-011-0817-z</doi><tpages>10</tpages></addata></record> |
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| ispartof | Molecular biology reports, 2012-02, Vol.39 (2), p.919-928 |
| issn | 0301-4851 1573-4978 |
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| subjects | Animal Anatomy Animal Biochemistry Animals Base Sequence Biomedical and Life Sciences Cattle - genetics DNA Primers - genetics Enhancers Gene expression Gene Expression Regulation - genetics Genetic Variation Guanylate cyclase Haplotypes Haplotypes - genetics Histology Life Sciences Linear Models Linkage Disequilibrium Molecular biology Molecular modelling Molecular Sequence Data Morphology Neuropeptide Y Neuropeptide Y - genetics Neuropeptide Y - metabolism Peptides Polymerase Chain Reaction Polymorphism Polymorphism, Single Nucleotide - genetics Promoter Regions, Genetic - genetics Promoters Protein Interaction Domains and Motifs - genetics Repressors Sequence Analysis, DNA Single-nucleotide polymorphism Sp1 protein Tata box TATA-binding protein Transcription factors |
| title | Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes |
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