Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss
The advent of functional genomics has sparked the interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, numerous biological processes remain understudied from this perspective, including intestinal immunity in farmed fish. The aim of this stud...
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| Veröffentlicht in: | Marine biotechnology (New York, N.Y.) N.Y.), 2017-06, Vol.19 (3), p.287-300 |
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| creator | Núñez-Acuña, Gustavo Détrée, Camille Gallardo-Escárate, Cristian Gonçalves, Ana Teresa |
| description | The advent of functional genomics has sparked the interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, numerous biological processes remain understudied from this perspective, including intestinal immunity in farmed fish. The aim of this study was to infer long non-coding RNA (lncRNAs) expression profiles in rainbow trout (
Oncorhynchus mykiss
) fed for 30 days with functional diets based on pre- and probiotics. For this, whole transcriptome sequencing was conducted through Illumina technology, and lncRNAs were mined to evaluate transcriptional activity in conjunction with known protein sequences. To detect differentially expressed transcripts, 880 novels and 9067 previously described
O. mykiss
lncRNAs were used. Expression levels and genome co-localization correlations with coding genes were also analyzed. Significant differences in gene expression were primarily found in the probiotic diet, which had a twofold downregulation of lncRNAs compared to other treatments. Notable differences by diet were also evidenced between the coding genes of distinct metabolic processes. In contrast, genome co-localization of lncRNAs with coding genes was similar for all diets. This study contributes novel knowledge regarding lncRNAs in fish, suggesting key roles in salmons fed with in-feed additives with the capacity to modulate the intestinal homeostasis and host health. |
| doi_str_mv | 10.1007/s10126-017-9750-z |
| format | Article |
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Oncorhynchus mykiss
) fed for 30 days with functional diets based on pre- and probiotics. For this, whole transcriptome sequencing was conducted through Illumina technology, and lncRNAs were mined to evaluate transcriptional activity in conjunction with known protein sequences. To detect differentially expressed transcripts, 880 novels and 9067 previously described
O. mykiss
lncRNAs were used. Expression levels and genome co-localization correlations with coding genes were also analyzed. Significant differences in gene expression were primarily found in the probiotic diet, which had a twofold downregulation of lncRNAs compared to other treatments. Notable differences by diet were also evidenced between the coding genes of distinct metabolic processes. In contrast, genome co-localization of lncRNAs with coding genes was similar for all diets. This study contributes novel knowledge regarding lncRNAs in fish, suggesting key roles in salmons fed with in-feed additives with the capacity to modulate the intestinal homeostasis and host health.</description><identifier>ISSN: 1436-2228</identifier><identifier>EISSN: 1436-2236</identifier><identifier>DOI: 10.1007/s10126-017-9750-z</identifier><identifier>PMID: 28500613</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Animal Feed - analysis ; Animals ; Aquaculture ; Biological activity ; Biomedical and Life Sciences ; Diet ; Diet - veterinary ; Engineering ; Feed additives ; Feeding ; Fish ; Fish culture ; Fish farms ; Freshwater & Marine Ecology ; Freshwater fishes ; Gene expression ; Genes ; Genome ; Genomes ; Genomics ; Homeostasis ; Immunity ; Intestine ; Intestines ; Intestines - metabolism ; Life Sciences ; Live feeds ; Localization ; Microbiology ; Non-coding RNA ; Oncorhynchus mykiss ; Oncorhynchus mykiss - genetics ; Oncorhynchus mykiss - metabolism ; Original Article ; Prebiotics - administration & dosage ; Probiotics ; Probiotics - administration & dosage ; Ribonucleic acid ; RNA ; RNA, Long Noncoding - genetics ; RNA, Long Noncoding - metabolism ; Salmon ; Transcription ; Transcriptome ; Trout ; Zoology</subject><ispartof>Marine biotechnology (New York, N.Y.), 2017-06, Vol.19 (3), p.287-300</ispartof><rights>Springer Science+Business Media New York 2017</rights><rights>Marine Biotechnology is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-6402a1e2fff86a536bd9b4ac7eb52a84ab538433f61733c7ef239f516af73f5d3</citedby><cites>FETCH-LOGICAL-c372t-6402a1e2fff86a536bd9b4ac7eb52a84ab538433f61733c7ef239f516af73f5d3</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/s10126-017-9750-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10126-017-9750-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,777,781,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28500613$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Núñez-Acuña, Gustavo</creatorcontrib><creatorcontrib>Détrée, Camille</creatorcontrib><creatorcontrib>Gallardo-Escárate, Cristian</creatorcontrib><creatorcontrib>Gonçalves, Ana Teresa</creatorcontrib><title>Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss</title><title>Marine biotechnology (New York, N.Y.)</title><addtitle>Mar Biotechnol</addtitle><addtitle>Mar Biotechnol (NY)</addtitle><description>The advent of functional genomics has sparked the interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, numerous biological processes remain understudied from this perspective, including intestinal immunity in farmed fish. The aim of this study was to infer long non-coding RNA (lncRNAs) expression profiles in rainbow trout (
Oncorhynchus mykiss
) fed for 30 days with functional diets based on pre- and probiotics. For this, whole transcriptome sequencing was conducted through Illumina technology, and lncRNAs were mined to evaluate transcriptional activity in conjunction with known protein sequences. To detect differentially expressed transcripts, 880 novels and 9067 previously described
O. mykiss
lncRNAs were used. Expression levels and genome co-localization correlations with coding genes were also analyzed. Significant differences in gene expression were primarily found in the probiotic diet, which had a twofold downregulation of lncRNAs compared to other treatments. Notable differences by diet were also evidenced between the coding genes of distinct metabolic processes. In contrast, genome co-localization of lncRNAs with coding genes was similar for all diets. This study contributes novel knowledge regarding lncRNAs in fish, suggesting key roles in salmons fed with in-feed additives with the capacity to modulate the intestinal homeostasis and host health.</description><subject>Animal Feed - analysis</subject><subject>Animals</subject><subject>Aquaculture</subject><subject>Biological activity</subject><subject>Biomedical and Life Sciences</subject><subject>Diet</subject><subject>Diet - veterinary</subject><subject>Engineering</subject><subject>Feed additives</subject><subject>Feeding</subject><subject>Fish</subject><subject>Fish culture</subject><subject>Fish farms</subject><subject>Freshwater & Marine Ecology</subject><subject>Freshwater fishes</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Homeostasis</subject><subject>Immunity</subject><subject>Intestine</subject><subject>Intestines</subject><subject>Intestines - metabolism</subject><subject>Life Sciences</subject><subject>Live feeds</subject><subject>Localization</subject><subject>Microbiology</subject><subject>Non-coding RNA</subject><subject>Oncorhynchus mykiss</subject><subject>Oncorhynchus mykiss - genetics</subject><subject>Oncorhynchus mykiss - metabolism</subject><subject>Original Article</subject><subject>Prebiotics - administration & dosage</subject><subject>Probiotics</subject><subject>Probiotics - administration & dosage</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Long Noncoding - 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Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss</title><author>Núñez-Acuña, Gustavo ; Détrée, Camille ; Gallardo-Escárate, Cristian ; Gonçalves, Ana Teresa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-6402a1e2fff86a536bd9b4ac7eb52a84ab538433f61733c7ef239f516af73f5d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animal Feed - analysis</topic><topic>Animals</topic><topic>Aquaculture</topic><topic>Biological activity</topic><topic>Biomedical and Life Sciences</topic><topic>Diet</topic><topic>Diet - veterinary</topic><topic>Engineering</topic><topic>Feed additives</topic><topic>Feeding</topic><topic>Fish</topic><topic>Fish culture</topic><topic>Fish farms</topic><topic>Freshwater & Marine Ecology</topic><topic>Freshwater fishes</topic><topic>Gene 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N.Y.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Núñez-Acuña, Gustavo</au><au>Détrée, Camille</au><au>Gallardo-Escárate, Cristian</au><au>Gonçalves, Ana Teresa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss</atitle><jtitle>Marine biotechnology (New York, N.Y.)</jtitle><stitle>Mar Biotechnol</stitle><addtitle>Mar Biotechnol (NY)</addtitle><date>2017-06-01</date><risdate>2017</risdate><volume>19</volume><issue>3</issue><spage>287</spage><epage>300</epage><pages>287-300</pages><issn>1436-2228</issn><eissn>1436-2236</eissn><abstract>The advent of functional genomics has sparked the interest in inferring the function of non-coding regions from the transcriptome in non-model species. However, numerous biological processes remain understudied from this perspective, including intestinal immunity in farmed fish. The aim of this study was to infer long non-coding RNA (lncRNAs) expression profiles in rainbow trout (
Oncorhynchus mykiss
) fed for 30 days with functional diets based on pre- and probiotics. For this, whole transcriptome sequencing was conducted through Illumina technology, and lncRNAs were mined to evaluate transcriptional activity in conjunction with known protein sequences. To detect differentially expressed transcripts, 880 novels and 9067 previously described
O. mykiss
lncRNAs were used. Expression levels and genome co-localization correlations with coding genes were also analyzed. Significant differences in gene expression were primarily found in the probiotic diet, which had a twofold downregulation of lncRNAs compared to other treatments. Notable differences by diet were also evidenced between the coding genes of distinct metabolic processes. In contrast, genome co-localization of lncRNAs with coding genes was similar for all diets. This study contributes novel knowledge regarding lncRNAs in fish, suggesting key roles in salmons fed with in-feed additives with the capacity to modulate the intestinal homeostasis and host health.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>28500613</pmid><doi>10.1007/s10126-017-9750-z</doi><tpages>14</tpages></addata></record> |
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| ispartof | Marine biotechnology (New York, N.Y.), 2017-06, Vol.19 (3), p.287-300 |
| issn | 1436-2228 1436-2236 |
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| source | MEDLINE; SpringerLink Journals |
| subjects | Animal Feed - analysis Animals Aquaculture Biological activity Biomedical and Life Sciences Diet Diet - veterinary Engineering Feed additives Feeding Fish Fish culture Fish farms Freshwater & Marine Ecology Freshwater fishes Gene expression Genes Genome Genomes Genomics Homeostasis Immunity Intestine Intestines Intestines - metabolism Life Sciences Live feeds Localization Microbiology Non-coding RNA Oncorhynchus mykiss Oncorhynchus mykiss - genetics Oncorhynchus mykiss - metabolism Original Article Prebiotics - administration & dosage Probiotics Probiotics - administration & dosage Ribonucleic acid RNA RNA, Long Noncoding - genetics RNA, Long Noncoding - metabolism Salmon Transcription Transcriptome Trout Zoology |
| title | Functional Diets Modulate lncRNA-Coding RNAs and Gene Interactions in the Intestine of Rainbow Trout Oncorhynchus mykiss |
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