Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)
Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as...
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| description | Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep. |
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MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0193371</identifier><identifier>PMID: 29489866</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Absorptivity ; Animals ; Apoptosis ; Biology and life sciences ; Biotechnology ; Cancer ; Cecum ; Colon ; Disease control ; Disease prevention ; Duodenum ; Editing ; Enrichment ; Gastrointestinal system ; Gene expression ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; Genes ; Genetic aspects ; Homeostasis ; Identification and classification ; Identification methods ; Intestine ; Intestines - metabolism ; Laboratories ; Medical research ; Medicine and Health Sciences ; Metabolism ; MicroRNA ; MicroRNAs ; MicroRNAs - genetics ; miRNA ; Next-generation sequencing ; Organ Specificity ; Ovis aries ; Rodents ; Sheep ; Small intestine ; Studies ; Target recognition ; Tissues ; Urial ; Writing</subject><ispartof>PloS one, 2018-02, Vol.13 (2), p.e0193371-e0193371</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Hou 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>2018 Hou et al 2018 Hou et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6071-a1571dded223375f428373690fd5a2205e318bc77449592009356927eff9586f3</citedby><cites>FETCH-LOGICAL-c6071-a1571dded223375f428373690fd5a2205e318bc77449592009356927eff9586f3</cites><orcidid>0000-0001-5678-8202</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/PMC5831392/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831392/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29489866$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Schubert, Michael</contributor><creatorcontrib>Hou, Lei</creatorcontrib><creatorcontrib>Ji, Zhibin</creatorcontrib><creatorcontrib>Wang, Guizhi</creatorcontrib><creatorcontrib>Wang, Jin</creatorcontrib><creatorcontrib>Chao, Tianle</creatorcontrib><creatorcontrib>Wang, Jianmin</creatorcontrib><title>Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. 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This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.</description><subject>Absorptivity</subject><subject>Animals</subject><subject>Apoptosis</subject><subject>Biology and life sciences</subject><subject>Biotechnology</subject><subject>Cancer</subject><subject>Cecum</subject><subject>Colon</subject><subject>Disease control</subject><subject>Disease prevention</subject><subject>Duodenum</subject><subject>Editing</subject><subject>Enrichment</subject><subject>Gastrointestinal system</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Homeostasis</subject><subject>Identification and classification</subject><subject>Identification methods</subject><subject>Intestine</subject><subject>Intestines - metabolism</subject><subject>Laboratories</subject><subject>Medical research</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>miRNA</subject><subject>Next-generation sequencing</subject><subject>Organ Specificity</subject><subject>Ovis aries</subject><subject>Rodents</subject><subject>Sheep</subject><subject>Small intestine</subject><subject>Studies</subject><subject>Target recognition</subject><subject>Tissues</subject><subject>Urial</subject><subject>Writing</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk9tu1DAQhiMEoqXwBggiIaH2Yhcf4ji-QVpVHFaqWKkcbs3UsTdeZeOt7VTA0-N002qDeoFy4dHkm9-e3-Mse4nRHFOO321c7zto5zvX6TnCgqbko-w4BWRWEkQfH8RH2bMQNggxWpXl0-yIiKISKTzOfi5r3UVrrIJoXZdDV-eqAQ8qam__7JPO5FurvLv8sgi57fLY6LREHaJNJ8ijDaHXYcBCo_UuP13d2JCDtzqcPc-eGGiDfjGuJ9n3jx--nX-eXaw-Lc8XFzNVIo5ngBnHda1rQlIjzBSkopyWApmaASGIaYqrK8V5UQgmCEKCslIQro0RrCoNPcle73V3rQtyNCfIgSREcCYSsdwTtYON3Hm7Bf9bOrDyNuH8WoKPVrVaGmJIXREGxuAi-QpUMQ4KEC2w0Lda78fd-qutrlXy0EM7EZ3-6Wwj1-5GsopiKkgSOB0FvLtO5kW5tUHptoVOu35_blZWXOCEvvkHfbi7kVpDasB2xqV91SAqF4wIikpWoUTNH6DSV-t0w2mSjE35ScHZpCAxUf-Ka-hDkMuvl__Prn5M2bcHbKOhjU1wbT_MW5iCxR5M8xeC1-beZIzk8BDu3JDDQ5DjQ0hlrw4v6L7obvLpX60yASQ</recordid><startdate>20180228</startdate><enddate>20180228</enddate><creator>Hou, Lei</creator><creator>Ji, Zhibin</creator><creator>Wang, Guizhi</creator><creator>Wang, Jin</creator><creator>Chao, Tianle</creator><creator>Wang, Jianmin</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>AEUYN</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>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-5678-8202</orcidid></search><sort><creationdate>20180228</creationdate><title>Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)</title><author>Hou, Lei ; Ji, Zhibin ; Wang, Guizhi ; Wang, Jin ; Chao, Tianle ; Wang, Jianmin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6071-a1571dded223375f428373690fd5a2205e318bc77449592009356927eff9586f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Absorptivity</topic><topic>Animals</topic><topic>Apoptosis</topic><topic>Biology and life sciences</topic><topic>Biotechnology</topic><topic>Cancer</topic><topic>Cecum</topic><topic>Colon</topic><topic>Disease control</topic><topic>Disease prevention</topic><topic>Duodenum</topic><topic>Editing</topic><topic>Enrichment</topic><topic>Gastrointestinal system</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Homeostasis</topic><topic>Identification and classification</topic><topic>Identification methods</topic><topic>Intestine</topic><topic>Intestines - 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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>Hou, Lei</au><au>Ji, Zhibin</au><au>Wang, Guizhi</au><au>Wang, Jin</au><au>Chao, Tianle</au><au>Wang, Jianmin</au><au>Schubert, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-02-28</date><risdate>2018</risdate><volume>13</volume><issue>2</issue><spage>e0193371</spage><epage>e0193371</epage><pages>e0193371-e0193371</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Sheep are small ruminants, and their long intestines exhibit high digestive and absorptive capacity in many different rearing conditions; however, the genetic bases of this characteristic remains unclear. MicroRNAs (miRNAs) play a major role in maintaining both intestinal morphological structure as well as in regulating the physiological functions of this organ. However, no study has reported on the miRNA expression profile in the intestinal tissues of sheep. Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 106 known miRNAs were identified, 458 conserved miRNAs were detected, 192 unannotated novel miRNAs were predicted, and 195 differentially expressed miRNAs were found between the different tissues. Additionally, 3,437 candidate target genes were predicted, and 17 non-redundant significantly enriched GO terms were identified using enrichment analysis. A total of 99 candidate target genes were found to significantly enriched in 4 KEGG biological pathways. A combined regulatory network was constructed based on 92 metabolism-related candidate target genes and 65 differentially expressed miRNAs, among which 7 miRNAs were identified as hub miRNAs. Via these mechanisms, miRNAs may play a role in maintaining intestinal homeostasis and metabolism. This study helps to further explain the mechanisms that underlie differences in tissue morphology and function in three intestinal segments of sheep.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29489866</pmid><doi>10.1371/journal.pone.0193371</doi><tpages>e0193371</tpages><orcidid>https://orcid.org/0000-0001-5678-8202</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Absorptivity Animals Apoptosis Biology and life sciences Biotechnology Cancer Cecum Colon Disease control Disease prevention Duodenum Editing Enrichment Gastrointestinal system Gene expression Gene Expression Profiling Gene Ontology Gene Regulatory Networks Genes Genetic aspects Homeostasis Identification and classification Identification methods Intestine Intestines - metabolism Laboratories Medical research Medicine and Health Sciences Metabolism MicroRNA MicroRNAs MicroRNAs - genetics miRNA Next-generation sequencing Organ Specificity Ovis aries Rodents Sheep Small intestine Studies Target recognition Tissues Urial Writing |
| title | Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries) |
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