The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio
Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles durin...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2021-01, Vol.113 (1), p.20-28 |
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| creator | Wang, Lanmei Song, Feibiao Zhu, Wenbin Fu, Jianjun Dong, Zaijie Xu, Pao |
| description | Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles during six main early development stages (2 h post-fertilization hpf, 6 hpf, 12 hpf, 20 hpf, 64 hpf and 1 day post-hatching). A total of 51,979 lncRNAs were identified. We screened the top 10 abundance lncRNAs and mRNAs and stage-specific lncRNAs and mRNAs (specificity measure SPM > 0.9). We identified significant differentially expressed lncRNAs and mRNAs (|log2 (fold change)| ≥ 1 and false discovery rate FDR of |
| doi_str_mv | 10.1016/j.ygeno.2020.11.025 |
| format | Article |
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•It provides the first lncRNA-mRNA expression profiles of six early stages in C. carpio.•We screened the stage-specific and differentially expressed lncRNAs and mRNAs.•LncRNA-mRNA co-regulated network analysis were investigated.•GO and KEGG analysis identified numerous signaling pathways.•It would advance the understanding of lncRNA-mediated mechanisms.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2020.11.025</identifier><identifier>PMID: 33271329</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Animals ; Carps - embryology ; Carps - genetics ; Carps - metabolism ; Common carp (Cyprinus carpio) ; Cyprinus carpio ; Danio rerio ; early development ; Embryonic development ; fish ; Gene Expression Regulation, Developmental ; gene ontology ; Gene Regulatory Networks ; genomics ; LncRNA ; mRNA ; non-coding RNA ; RNA, Long Noncoding - genetics ; RNA, Long Noncoding - metabolism ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Stage-specific expression ; troponin T</subject><ispartof>Genomics (San Diego, Calif.), 2021-01, Vol.113 (1), p.20-28</ispartof><rights>2020 Elsevier Inc.</rights><rights>Copyright © 2020 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c487t-128e120408a5fd4e6cbb96dc4aa3768bf8ddeca81e30601c32b175cfe3f91eb53</citedby><cites>FETCH-LOGICAL-c487t-128e120408a5fd4e6cbb96dc4aa3768bf8ddeca81e30601c32b175cfe3f91eb53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0888754320320292$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33271329$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Lanmei</creatorcontrib><creatorcontrib>Song, Feibiao</creatorcontrib><creatorcontrib>Zhu, Wenbin</creatorcontrib><creatorcontrib>Fu, Jianjun</creatorcontrib><creatorcontrib>Dong, Zaijie</creatorcontrib><creatorcontrib>Xu, Pao</creatorcontrib><title>The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles during six main early development stages (2 h post-fertilization hpf, 6 hpf, 12 hpf, 20 hpf, 64 hpf and 1 day post-hatching). A total of 51,979 lncRNAs were identified. We screened the top 10 abundance lncRNAs and mRNAs and stage-specific lncRNAs and mRNAs (specificity measure SPM > 0.9). We identified significant differentially expressed lncRNAs and mRNAs (|log2 (fold change)| ≥ 1 and false discovery rate FDR of <0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified numerous signaling pathways. Additionally, the lncRNA-mRNA co-regulated network analysis of two lncRNAs (lncrps25 and malat1) and two mRNAs (mitf and troponin T) were investigated. Our results provide new insight into the role of lncRNAs and mRNAs, and would advance the understanding of lncRNA-mediated mechanisms in early development of fish.
•It provides the first lncRNA-mRNA expression profiles of six early stages in C. carpio.•We screened the stage-specific and differentially expressed lncRNAs and mRNAs.•LncRNA-mRNA co-regulated network analysis were investigated.•GO and KEGG analysis identified numerous signaling pathways.•It would advance the understanding of lncRNA-mediated mechanisms.</description><subject>Animals</subject><subject>Carps - embryology</subject><subject>Carps - genetics</subject><subject>Carps - metabolism</subject><subject>Common carp (Cyprinus carpio)</subject><subject>Cyprinus carpio</subject><subject>Danio rerio</subject><subject>early development</subject><subject>Embryonic development</subject><subject>fish</subject><subject>Gene Expression Regulation, Developmental</subject><subject>gene ontology</subject><subject>Gene Regulatory Networks</subject><subject>genomics</subject><subject>LncRNA</subject><subject>mRNA</subject><subject>non-coding RNA</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Long Noncoding - metabolism</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>Stage-specific expression</subject><subject>troponin T</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkctu1DAUhi0EokPhCZCQlyzI4FscZ8GiGnGTKipVZW059sngUWIHO6mUF-hz45kpLOnKx_b3-8jnQ-gtJVtKqPx42K57CHHLCCsndEtY_QxtKFFtpaSQz9GGKKWqphb8Ar3K-UAIabliL9EF56yhnLUb9HD3C3CezR6qPIH1vbd4iGGPQwyVjc6X8vbHVcYmODyeKu8gzEfQzD6G04UJZlizz9gt6ZgAk4YVO7iHIU5jwXHssY3jWHhr0vQB79apkEs-bX18jV70Zsjw5nG9RD-_fL7bfauub75-311dV1aoZq4oU0AZEUSZuncCpO26VjorjOGNVF2vnANrFAVOJKGWs442te2B9y2FruaX6P353SnF3wvkWY8-WxgGEyAuWbOaCSYaIdnTqJCNpE0ZdUH5GbUp5pyg1-Vzo0mrpkQfXemDPrnSR1eaUl1cldS7xwZLN4L7l_krpwCfzgCUidx7SDpbD8GC8wnsrF30_23wB7vcqCw</recordid><startdate>202101</startdate><enddate>202101</enddate><creator>Wang, Lanmei</creator><creator>Song, Feibiao</creator><creator>Zhu, Wenbin</creator><creator>Fu, Jianjun</creator><creator>Dong, Zaijie</creator><creator>Xu, Pao</creator><general>Elsevier Inc</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>7X8</scope><scope>7S9</scope><scope>L.6</scope></search><sort><creationdate>202101</creationdate><title>The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio</title><author>Wang, Lanmei ; Song, Feibiao ; Zhu, Wenbin ; Fu, Jianjun ; Dong, Zaijie ; Xu, Pao</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c487t-128e120408a5fd4e6cbb96dc4aa3768bf8ddeca81e30601c32b175cfe3f91eb53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Animals</topic><topic>Carps - embryology</topic><topic>Carps - genetics</topic><topic>Carps - metabolism</topic><topic>Common carp (Cyprinus carpio)</topic><topic>Cyprinus carpio</topic><topic>Danio rerio</topic><topic>early development</topic><topic>Embryonic development</topic><topic>fish</topic><topic>Gene Expression Regulation, Developmental</topic><topic>gene ontology</topic><topic>Gene Regulatory Networks</topic><topic>genomics</topic><topic>LncRNA</topic><topic>mRNA</topic><topic>non-coding RNA</topic><topic>RNA, Long Noncoding - genetics</topic><topic>RNA, Long Noncoding - metabolism</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>Stage-specific expression</topic><topic>troponin T</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Lanmei</creatorcontrib><creatorcontrib>Song, Feibiao</creatorcontrib><creatorcontrib>Zhu, Wenbin</creatorcontrib><creatorcontrib>Fu, Jianjun</creatorcontrib><creatorcontrib>Dong, Zaijie</creatorcontrib><creatorcontrib>Xu, Pao</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Lanmei</au><au>Song, Feibiao</au><au>Zhu, Wenbin</au><au>Fu, Jianjun</au><au>Dong, Zaijie</au><au>Xu, Pao</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2021-01</date><risdate>2021</risdate><volume>113</volume><issue>1</issue><spage>20</spage><epage>28</epage><pages>20-28</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles during six main early development stages (2 h post-fertilization hpf, 6 hpf, 12 hpf, 20 hpf, 64 hpf and 1 day post-hatching). A total of 51,979 lncRNAs were identified. We screened the top 10 abundance lncRNAs and mRNAs and stage-specific lncRNAs and mRNAs (specificity measure SPM > 0.9). We identified significant differentially expressed lncRNAs and mRNAs (|log2 (fold change)| ≥ 1 and false discovery rate FDR of <0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified numerous signaling pathways. Additionally, the lncRNA-mRNA co-regulated network analysis of two lncRNAs (lncrps25 and malat1) and two mRNAs (mitf and troponin T) were investigated. Our results provide new insight into the role of lncRNAs and mRNAs, and would advance the understanding of lncRNA-mediated mechanisms in early development of fish.
•It provides the first lncRNA-mRNA expression profiles of six early stages in C. carpio.•We screened the stage-specific and differentially expressed lncRNAs and mRNAs.•LncRNA-mRNA co-regulated network analysis were investigated.•GO and KEGG analysis identified numerous signaling pathways.•It would advance the understanding of lncRNA-mediated mechanisms.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>33271329</pmid><doi>10.1016/j.ygeno.2020.11.025</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Carps - embryology Carps - genetics Carps - metabolism Common carp (Cyprinus carpio) Cyprinus carpio Danio rerio early development Embryonic development fish Gene Expression Regulation, Developmental gene ontology Gene Regulatory Networks genomics LncRNA mRNA non-coding RNA RNA, Long Noncoding - genetics RNA, Long Noncoding - metabolism RNA, Messenger - genetics RNA, Messenger - metabolism Stage-specific expression troponin T |
| title | The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio |
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