Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)
The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly under...
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| description | The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp. |
| doi_str_mv | 10.1371/journal.pone.0266189 |
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MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0266189</identifier><identifier>PMID: 35344574</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animal sciences ; Animals ; Aquaculture ; Biology and life sciences ; Carp ; Carps - genetics ; Carps - metabolism ; Cell differentiation ; Cell proliferation ; Ctenopharyngodon idella ; Developmental stages ; Differentiation ; Encyclopedias ; Epidemics ; Erythrocytes ; Fish ; Genetic aspects ; Genomes ; Grasses ; Health aspects ; Immune response ; Immune system ; Infectious diseases ; Invertebrates ; Laboratories ; Lipid metabolism ; Lipids ; Lymphocytes ; Lymphocytes T ; Metabolism ; MicroRNA ; MicroRNAs ; MicroRNAs - genetics ; MicroRNAs - metabolism ; miRNA ; Molecular biology ; Networks ; Peroxisome proliferator-activated receptors ; Physiological aspects ; Physiology ; Receptors ; RNA, Messenger ; Signal transduction ; Signaling ; Spleen ; Spleen - metabolism ; T cell receptors ; T-cell receptor ; Tissues ; Transcriptomes ; Vertebrates ; Zoology</subject><ispartof>PloS one, 2022-03, Vol.17 (3), p.e0266189-e0266189</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Zhao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Zhao et al 2022 Zhao et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c622t-afc25d7f4edfc2c917db57be3c874195322c0cd21404b0da31179b665ee86b523</citedby><cites>FETCH-LOGICAL-c622t-afc25d7f4edfc2c917db57be3c874195322c0cd21404b0da31179b665ee86b523</cites><orcidid>0000-0001-8442-8861</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/PMC8959171/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8959171/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35344574$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Anbazhagan, Rajakumar</contributor><creatorcontrib>Zhao, Yinli</creatorcontrib><creatorcontrib>Fan, Shengxin</creatorcontrib><creatorcontrib>Yuan, Pengtao</creatorcontrib><creatorcontrib>Li, Guoxi</creatorcontrib><title>Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp.</description><subject>Animal sciences</subject><subject>Animals</subject><subject>Aquaculture</subject><subject>Biology and life sciences</subject><subject>Carp</subject><subject>Carps - genetics</subject><subject>Carps - metabolism</subject><subject>Cell differentiation</subject><subject>Cell proliferation</subject><subject>Ctenopharyngodon idella</subject><subject>Developmental stages</subject><subject>Differentiation</subject><subject>Encyclopedias</subject><subject>Epidemics</subject><subject>Erythrocytes</subject><subject>Fish</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Grasses</subject><subject>Health aspects</subject><subject>Immune response</subject><subject>Immune system</subject><subject>Infectious diseases</subject><subject>Invertebrates</subject><subject>Laboratories</subject><subject>Lipid metabolism</subject><subject>Lipids</subject><subject>Lymphocytes</subject><subject>Lymphocytes T</subject><subject>Metabolism</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>Molecular biology</subject><subject>Networks</subject><subject>Peroxisome proliferator-activated receptors</subject><subject>Physiological aspects</subject><subject>Physiology</subject><subject>Receptors</subject><subject>RNA, Messenger</subject><subject>Signal transduction</subject><subject>Signaling</subject><subject>Spleen</subject><subject>Spleen - metabolism</subject><subject>T cell receptors</subject><subject>T-cell receptor</subject><subject>Tissues</subject><subject>Transcriptomes</subject><subject>Vertebrates</subject><subject>Zoology</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</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><sourceid>DOA</sourceid><recordid>eNqNk11v0zAUhiMEYmPwDxBEQkLbRYu_4iQ3SFU1oNLEpPFxazm207qkdmYnMPj1nKzZ1KBdoFzEPn7O6-PXPknyEqM5pjl-t_V9cLKZt96ZOSKc46J8lBzjkpIZJ4g-PhgfJc9i3CKU0YLzp8kRzShjWc6Okz_nN20wMVrvUrWRQarOBBs7q2IqnU6tgzkEh3Vnul8-_Iipr9OdVcFffV5EINLYNsa4tLMx9uZ2eR1kjKmSoU1Pl51xvgXt327tNehYbZpGnj1PntSyiebF-D9Jvn04_7r8NLu4_LhaLi5mihPSzWStSKbzmhkNI1XiXFdZXhmqipzhMqOEKKQ0wQyxCmlJMc7LivPMmIJXGaEnyeu9btv4KEbboiCcMUrLgmEgVntCe7kVbbA7KFZ4acVtwIe1kAEsaYzQFS0I1zmUgBjSWSlNVVe6IIwgVhINWu_H3fpqZ7QyrguymYhOV5zdiLX_KYoyg7MNxZyOAsFfg52d2NmoBsec8f2-7pITuEJA3_yDPny6kVpLOIB1tYd91SAqFrwsMkY4HVyaP0DBpw3cNbyx2kJ8knA2SQCmMzfdWvYxitWXq_9nL79P2bcH7MbIpttE3_TDE4xTkO1BeIkxBlPfm4yRGFrkzg0xtIgYWwTSXh1e0H3SXU_Qv7DXDak</recordid><startdate>20220328</startdate><enddate>20220328</enddate><creator>Zhao, Yinli</creator><creator>Fan, Shengxin</creator><creator>Yuan, Pengtao</creator><creator>Li, Guoxi</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-8442-8861</orcidid></search><sort><creationdate>20220328</creationdate><title>Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)</title><author>Zhao, Yinli ; Fan, Shengxin ; Yuan, Pengtao ; Li, Guoxi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c622t-afc25d7f4edfc2c917db57be3c874195322c0cd21404b0da31179b665ee86b523</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animal sciences</topic><topic>Animals</topic><topic>Aquaculture</topic><topic>Biology and life sciences</topic><topic>Carp</topic><topic>Carps - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhao, Yinli</au><au>Fan, Shengxin</au><au>Yuan, Pengtao</au><au>Li, Guoxi</au><au>Anbazhagan, Rajakumar</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2022-03-28</date><risdate>2022</risdate><volume>17</volume><issue>3</issue><spage>e0266189</spage><epage>e0266189</epage><pages>e0266189-e0266189</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The spleen is an important immune organ in fish. MicroRNAs (miRNAs) have been shown to play an important role in the regulation of immune function. However, miRNA expression profiles and their interaction networks associated with the postnatal late development of spleen tissue are still poorly understood in fish. The grass carp (Ctenopharyngodon idella) is an important economic aquaculture species in China. Here, two small RNA libraries were constructed from the spleen tissue of healthy grass carp at one-year-old and three-year-old. A total of 324 known conserved miRNAs and 9 novel miRNAs were identified by using bioinformatic analysis. Family analysis showed that 23 families such as let-7, mir-1, mir-10, mir-124, mir-8, mir-7, mir-9, and mir-153 were highly conserved between vertebrates and invertebrates. In addition, 14 families such as mir-459, mir-430, mir-462, mir-7147, mir-2187, and mir-722 were present only in fish. Expression analysis showed that the expression patterns of miRNAs in the spleen of one-year-old and three-year-old grass carp were highly consistent, and the percentage of miRNAs with TPM > 100 was above 39%. Twenty significant differentially expressed (SDE) miRNAs were identified. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that these SDE miRNAs were primarily involved in erythrocyte differentiation, lymphoid organ development, immune response, lipid metabolic process, the B cell receptor signaling pathway, the T cell receptor signaling pathway, and the PPAR signaling pathway. In addition, the following miRNA-mRNA interaction networks were constructed: immune and hematopoietic, cell proliferation and differentiation, and lipid metabolism. This study determined the miRNA transcriptome as well as miRNA-mRNA interaction networks in normal spleen tissue during the late development stages of grass carp. The results expand the number of known miRNAs in grass carp and are a valuable resource for better understanding the molecular biology of the spleen development in grass carp.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35344574</pmid><doi>10.1371/journal.pone.0266189</doi><tpages>e0266189</tpages><orcidid>https://orcid.org/0000-0001-8442-8861</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Free E-Journal (出版社公開部分のみ）; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animal sciences Animals Aquaculture Biology and life sciences Carp Carps - genetics Carps - metabolism Cell differentiation Cell proliferation Ctenopharyngodon idella Developmental stages Differentiation Encyclopedias Epidemics Erythrocytes Fish Genetic aspects Genomes Grasses Health aspects Immune response Immune system Infectious diseases Invertebrates Laboratories Lipid metabolism Lipids Lymphocytes Lymphocytes T Metabolism MicroRNA MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism miRNA Molecular biology Networks Peroxisome proliferator-activated receptors Physiological aspects Physiology Receptors RNA, Messenger Signal transduction Signaling Spleen Spleen - metabolism T cell receptors T-cell receptor Tissues Transcriptomes Vertebrates Zoology |
| title | Expression characteristics and interaction networks of microRNAs in spleen tissues of grass carp (Ctenopharyngodon idella) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T08%3A09%3A53IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Expression%20characteristics%20and%20interaction%20networks%20of%20microRNAs%20in%20spleen%20tissues%20of%20grass%20carp%20(Ctenopharyngodon%20idella)&rft.jtitle=PloS%20one&rft.au=Zhao,%20Yinli&rft.date=2022-03-28&rft.volume=17&rft.issue=3&rft.spage=e0266189&rft.epage=e0266189&rft.pages=e0266189-e0266189&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0266189&rft_dat=%3Cgale_plos_%3EA698542632%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2644339841&rft_id=info:pmid/35344574&rft_galeid=A698542632&rft_doaj_id=oai_doaj_org_article_db3826d7b57040d59aebfbd82420492d&rfr_iscdi=true |