Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes
Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transc...
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| Veröffentlicht in: | BMC genetics 2021-02, Vol.22 (1), p.9-9, Article 9 |
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| description | Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB(BB) (MM) and FecB(++) (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy. |
| doi_str_mv | 10.1186/s12863-020-00957-w |
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However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB(BB) (MM) and FecB(++) (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.</description><identifier>ISSN: 2730-6844</identifier><identifier>EISSN: 2730-6844</identifier><identifier>EISSN: 1471-2156</identifier><identifier>DOI: 10.1186/s12863-020-00957-w</identifier><identifier>PMID: 33602139</identifier><language>eng</language><publisher>LONDON: Springer Nature</publisher><subject>Analysis ; Animals ; Antisense RNA ; Cell adhesion & migration ; Cell cycle ; Circadian rhythms ; Correlation analysis ; Diseases ; Endocrine system ; Fecundity ; Female ; Follicular Phase - genetics ; Gene expression ; Gene mutations ; Genes ; Genetic aspects ; Genetics & Heredity ; Genomes ; Genotype ; Genotypes ; Growth ; Health aspects ; Hypothalamus ; Life Sciences & Biomedicine ; Luteal Phase - genetics ; Mammals ; Messenger RNA ; Metabolism ; Mutation ; Ovaries ; Phototransduction ; Pineal gland ; Pineal Gland - metabolism ; Pituitary ; Proteins ; RAG2 protein ; RNA polymerase ; RNA sequencing ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; Science & Technology ; Sheep ; Sheep - genetics ; Signal transduction ; Transcriptome ; Transcriptomes</subject><ispartof>BMC genetics, 2021-02, Vol.22 (1), p.9-9, Article 9</ispartof><rights>COPYRIGHT 2021 BioMed Central Ltd.</rights><rights>2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s) 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>5</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000620970800002</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c565t-75475dc800db7dfa429e354b05dcf34b503758889b9fe25d6058c18600d9d9043</citedby><cites>FETCH-LOGICAL-c565t-75475dc800db7dfa429e354b05dcf34b503758889b9fe25d6058c18600d9d9043</cites><orcidid>0000-0002-5164-0310</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/PMC7893892/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893892/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2115,27929,27930,39263,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33602139$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Chunyan</creatorcontrib><creatorcontrib>He, Xiaoyun</creatorcontrib><creatorcontrib>Zhang, Zijun</creatorcontrib><creatorcontrib>Ren, Chunhuan</creatorcontrib><creatorcontrib>Chu, Mingxing</creatorcontrib><title>Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes</title><title>BMC genetics</title><addtitle>BMC GENOMIC DATA</addtitle><addtitle>BMC Genom Data</addtitle><description>Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB(BB) (MM) and FecB(++) (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.</description><subject>Analysis</subject><subject>Animals</subject><subject>Antisense RNA</subject><subject>Cell adhesion & migration</subject><subject>Cell cycle</subject><subject>Circadian rhythms</subject><subject>Correlation analysis</subject><subject>Diseases</subject><subject>Endocrine system</subject><subject>Fecundity</subject><subject>Female</subject><subject>Follicular Phase - genetics</subject><subject>Gene expression</subject><subject>Gene mutations</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetics & Heredity</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Growth</subject><subject>Health aspects</subject><subject>Hypothalamus</subject><subject>Life Sciences & Biomedicine</subject><subject>Luteal Phase - genetics</subject><subject>Mammals</subject><subject>Messenger RNA</subject><subject>Metabolism</subject><subject>Mutation</subject><subject>Ovaries</subject><subject>Phototransduction</subject><subject>Pineal gland</subject><subject>Pineal Gland - metabolism</subject><subject>Pituitary</subject><subject>Proteins</subject><subject>RAG2 protein</subject><subject>RNA polymerase</subject><subject>RNA sequencing</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Messenger - genetics</subject><subject>Science & Technology</subject><subject>Sheep</subject><subject>Sheep - genetics</subject><subject>Signal transduction</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><issn>2730-6844</issn><issn>2730-6844</issn><issn>1471-2156</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>HGBXW</sourceid><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>eNqNksFu1DAQhiMEolXpC3BAlriAUMrEiZP4glRWlFaqKGoLVyvrTLKusvZiO136Jjwuk24pXcSh8sGW_f3_yDN_krzM4CDL6vJ9yHhd5ilwSAGkqNL1k2SXVzmkZV0UTx-cd5L9EK4AgIss5wKeJzt5XgLPcrmb_PpqLDYD64fGtiz6xgbtzSq6pdFs5V1nBmN75vGaqMDiAllrug492mhI57EfhyYaZ5nr2GD1-ZdDNlktp4NHekPydZPXYDqjG33DjGUXl8csLBBXbG3igsW1Y0eoP7IerYs3KwwvkmcdVcT9u30v-Xb06XJ2nJ6efT6ZHZ6mWpQippUoKtHqGqCdV23XFFxiLoo50GWXF3MBeSXqupZz2SEXbQmi1tQ_4mUrocj3kg8b39U4X2Kr6V--GdTKm2Xjb5RrjNp-sWahenetqlrmteRk8ObOwLsfI4aoliZoHKih6MageCEzKYDLitDX_6BXbvSWvjdRIKXgAH-pvhlQGds5qqsnU3U4FS2h4lPZg_9QtFqk0TmLNDncFrzdEhAT8WfsmzEEdXJx_nj27Ps2yzes9i4Ej9197zJQU1TVJqqKoqpuo6rWJHr1sOv3kj_BJKDeAGucuy5og1bjPUZhLjnICmjulOuZibcRnLnRRpK-e7w0_w29hQPW</recordid><startdate>20210218</startdate><enddate>20210218</enddate><creator>Li, Chunyan</creator><creator>He, Xiaoyun</creator><creator>Zhang, Zijun</creator><creator>Ren, Chunhuan</creator><creator>Chu, Mingxing</creator><general>Springer Nature</general><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>BLEPL</scope><scope>DTL</scope><scope>HGBXW</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</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>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>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/0000-0002-5164-0310</orcidid></search><sort><creationdate>20210218</creationdate><title>Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes</title><author>Li, Chunyan ; He, Xiaoyun ; Zhang, Zijun ; Ren, Chunhuan ; Chu, Mingxing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c565t-75475dc800db7dfa429e354b05dcf34b503758889b9fe25d6058c18600d9d9043</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Antisense RNA</topic><topic>Cell adhesion & migration</topic><topic>Cell cycle</topic><topic>Circadian rhythms</topic><topic>Correlation analysis</topic><topic>Diseases</topic><topic>Endocrine system</topic><topic>Fecundity</topic><topic>Female</topic><topic>Follicular Phase - genetics</topic><topic>Gene expression</topic><topic>Gene mutations</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetics & Heredity</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Growth</topic><topic>Health aspects</topic><topic>Hypothalamus</topic><topic>Life Sciences & Biomedicine</topic><topic>Luteal Phase - genetics</topic><topic>Mammals</topic><topic>Messenger RNA</topic><topic>Metabolism</topic><topic>Mutation</topic><topic>Ovaries</topic><topic>Phototransduction</topic><topic>Pineal gland</topic><topic>Pineal Gland - metabolism</topic><topic>Pituitary</topic><topic>Proteins</topic><topic>RAG2 protein</topic><topic>RNA polymerase</topic><topic>RNA sequencing</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Messenger - genetics</topic><topic>Science & Technology</topic><topic>Sheep</topic><topic>Sheep - genetics</topic><topic>Signal transduction</topic><topic>Transcriptome</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Chunyan</creatorcontrib><creatorcontrib>He, Xiaoyun</creatorcontrib><creatorcontrib>Zhang, Zijun</creatorcontrib><creatorcontrib>Ren, Chunhuan</creatorcontrib><creatorcontrib>Chu, Mingxing</creatorcontrib><collection>Web of Science Core Collection</collection><collection>Science Citation Index Expanded</collection><collection>Web of Science - Science Citation Index Expanded - 2021</collection><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: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences 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 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>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 genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Chunyan</au><au>He, Xiaoyun</au><au>Zhang, Zijun</au><au>Ren, Chunhuan</au><au>Chu, Mingxing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes</atitle><jtitle>BMC genetics</jtitle><stitle>BMC GENOMIC DATA</stitle><addtitle>BMC Genom Data</addtitle><date>2021-02-18</date><risdate>2021</risdate><volume>22</volume><issue>1</issue><spage>9</spage><epage>9</epage><pages>9-9</pages><artnum>9</artnum><issn>2730-6844</issn><eissn>2730-6844</eissn><eissn>1471-2156</eissn><abstract>Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB(BB) (MM) and FecB(++) (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.</abstract><cop>LONDON</cop><pub>Springer Nature</pub><pmid>33602139</pmid><doi>10.1186/s12863-020-00957-w</doi><tpages>17</tpages><orcidid>https://orcid.org/0000-0002-5164-0310</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Animals Antisense RNA Cell adhesion & migration Cell cycle Circadian rhythms Correlation analysis Diseases Endocrine system Fecundity Female Follicular Phase - genetics Gene expression Gene mutations Genes Genetic aspects Genetics & Heredity Genomes Genotype Genotypes Growth Health aspects Hypothalamus Life Sciences & Biomedicine Luteal Phase - genetics Mammals Messenger RNA Metabolism Mutation Ovaries Phototransduction Pineal gland Pineal Gland - metabolism Pituitary Proteins RAG2 protein RNA polymerase RNA sequencing RNA, Long Noncoding - genetics RNA, Messenger - genetics Science & Technology Sheep Sheep - genetics Signal transduction Transcriptome Transcriptomes |
| title | Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes |
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