High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.

The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excre...

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Autores principales:	Muyan Chen, Xiumei Zhang, Jianning Liu, Kenneth B Storey
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a372c6905d764f51a280f57102e88d53
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spelling	oai:doaj.org-article:a372c6905d764f51a280f57102e88d532021-11-18T08:51:03ZHigh-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.1932-620310.1371/journal.pone.0076120https://doaj.org/article/a372c6905d764f51a280f57102e88d532013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24143179/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of the sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. We identified 308 sea cucumber miRNAs, including 18 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to the active state). We identified 42 differentially expressed miRNAs [RPM (reads per million) >10, \|FC\| (\|fold change\|) ≥ 1, FDR (false discovery rate) <0.01] during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes and GO analysis suggest that these miRNAs could play important roles in global transcriptional depression and cell differentiation during aestivation. High-throughput sequencing data and microarray data have been submitted to GEO database.Muyan ChenXiumei ZhangJianning LiuKenneth B StoreyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e76120 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Muyan Chen Xiumei Zhang Jianning Liu Kenneth B Storey High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
description	The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of the sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. We identified 308 sea cucumber miRNAs, including 18 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to the active state). We identified 42 differentially expressed miRNAs [RPM (reads per million) >10, \|FC\| (\|fold change\|) ≥ 1, FDR (false discovery rate) <0.01] during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes and GO analysis suggest that these miRNAs could play important roles in global transcriptional depression and cell differentiation during aestivation. High-throughput sequencing data and microarray data have been submitted to GEO database.
format	article
author	Muyan Chen Xiumei Zhang Jianning Liu Kenneth B Storey
author_facet	Muyan Chen Xiumei Zhang Jianning Liu Kenneth B Storey
author_sort	Muyan Chen
title	High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
title_short	High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
title_full	High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
title_fullStr	High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
title_full_unstemmed	High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
title_sort	high-throughput sequencing reveals differential expression of mirnas in intestine from sea cucumber during aestivation.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/a372c6905d764f51a280f57102e88d53
work_keys_str_mv	AT muyanchen highthroughputsequencingrevealsdifferentialexpressionofmirnasinintestinefromseacucumberduringaestivation AT xiumeizhang highthroughputsequencingrevealsdifferentialexpressionofmirnasinintestinefromseacucumberduringaestivation AT jianningliu highthroughputsequencingrevealsdifferentialexpressionofmirnasinintestinefromseacucumberduringaestivation AT kennethbstorey highthroughputsequencingrevealsdifferentialexpressionofmirnasinintestinefromseacucumberduringaestivation
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High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.

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