Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver

Abstract RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ruobing Liang, Bo Han, Qian Li, Yuwei Yuan, Jianguo Li, Dongxiao Sun
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ddf527090fad4f9281d85dff118c5301
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:ddf527090fad4f9281d85dff118c5301
record_format	dspace
spelling	oai:doaj.org-article:ddf527090fad4f9281d85dff118c53012021-12-02T11:52:40ZUsing RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver10.1038/s41598-017-06634-w2045-2322https://doaj.org/article/ddf527090fad4f9281d85dff118c53012017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06634-whttps://doaj.org/toc/2045-2322Abstract RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.Ruobing LiangBo HanQian LiYuwei YuanJianguo LiDongxiao SunNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ruobing Liang Bo Han Qian Li Yuwei Yuan Jianguo Li Dongxiao Sun Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
description	Abstract RNA sequencing has been extensively used to study specific gene expression patterns to discover potential key genes related to complex traits of interest in animals. Of note, a new regulatory mechanism builds a large-scale regulatory network among transcriptome, where lncRNAs act as competing endogenous RNAs (ceRNAs) to sponge miRNAs to regulate the expression of miRNA target genes post-transcriptionally. In this study, we sequenced the cDNA and sRNA libraries of nine liver samples from three Holstein cows during dry period, early lactation, and peak of lactation with HiSeq platform. As a result, we identified 665 genes, 57 miRNAs and 33 lncRNAs that displayed differential expression patterns across periods. Subsequently, a total of 41ceRNA pairs (lncRNA-mRNA) sharing 11 miRNAs were constructed including 30 differentially expressed genes. Importantly, 12 among them were presented in our large metabolic networks, and predicted to influence the lipid metabolism through insulin, PI3K-Akt, MAPK, AMPK, mTOR, and PPAR signaling pathways, thus, these genes were considered as the most promising candidates for milk fat formation. To our knowledge, this is first investigation to profile the ceRNA regulatory networks of liver transcriptome that could affect milk fat synthesis in bovine, providing a new view of the regulatory mechanism of RNAs.
format	article
author	Ruobing Liang Bo Han Qian Li Yuwei Yuan Jianguo Li Dongxiao Sun
author_facet	Ruobing Liang Bo Han Qian Li Yuwei Yuan Jianguo Li Dongxiao Sun
author_sort	Ruobing Liang
title	Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
title_short	Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
title_full	Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
title_fullStr	Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
title_full_unstemmed	Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver
title_sort	using rna sequencing to identify putative competing endogenous rnas (cernas) potentially regulating fat metabolism in bovine liver
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/ddf527090fad4f9281d85dff118c5301
work_keys_str_mv	AT ruobingliang usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver AT bohan usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver AT qianli usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver AT yuweiyuan usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver AT jianguoli usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver AT dongxiaosun usingrnasequencingtoidentifyputativecompetingendogenousrnascernaspotentiallyregulatingfatmetabolisminbovineliver
_version_	1718395015506427904

Using RNA sequencing to identify putative competing endogenous RNAs (ceRNAs) potentially regulating fat metabolism in bovine liver

Ejemplares similares