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Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii

Subterranean rodents could maintain their normal activities in hypoxic environments underground. Eospalax fontanierii, as one kind of subterranean rodent found in China can survive very low oxygen concentration in labs. It has been demonstrated that long non-coding RNAs (lncRNAs) have important role...

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Autores principales: Hao, Zhiqiang, Han, Mingfang, Guo, Juanjuan, Li, Guanglin, He, Jianping, Li, Jingang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8929107/
https://www.ncbi.nlm.nih.gov/pubmed/34889903
http://dx.doi.org/10.3390/cimb43030132
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author Hao, Zhiqiang
Han, Mingfang
Guo, Juanjuan
Li, Guanglin
He, Jianping
Li, Jingang
author_facet Hao, Zhiqiang
Han, Mingfang
Guo, Juanjuan
Li, Guanglin
He, Jianping
Li, Jingang
author_sort Hao, Zhiqiang
collection PubMed
description Subterranean rodents could maintain their normal activities in hypoxic environments underground. Eospalax fontanierii, as one kind of subterranean rodent found in China can survive very low oxygen concentration in labs. It has been demonstrated that long non-coding RNAs (lncRNAs) have important roles in gene expression regulations at different levels and some lncRNAs were found as hypoxia-regulated lncRNAs in cancers. We predicted thousands of lncRNAs in the liver and heart tissues by analyzing RNA-Seq data in Eospalax fontanierii. Those lncRNAs often have shorter lengths, lower expression levels, and lower GC contents than mRNAs. Majors of lncRNAs have expression peaks in hypoxia conditions. We found 1128 DE-lncRNAs (differential expressed lncRNAs) responding to hypoxia. To search the miRNA regulation network for lncRNAs, we predicted 471 and 92 DE-lncRNAs acting as potential miRNA target and target mimics, respectively. We also predicted the functions of DE-lncRNAs based on the co-expression networks of lncRNA-mRNA. The DE-lncRNAs participated in the functions of biological regulation, signaling, development, oxoacid metabolic process, lipid metabolic/biosynthetic process, and catalytic activity. As the first study of lncRNAs in Eospalax fontanierii, our results show that lncRNAs are popular in transcriptome widely and can participate in multiple biological processes in hypoxia responses.
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spelling pubmed-89291072022-06-04 Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii Hao, Zhiqiang Han, Mingfang Guo, Juanjuan Li, Guanglin He, Jianping Li, Jingang Curr Issues Mol Biol Article Subterranean rodents could maintain their normal activities in hypoxic environments underground. Eospalax fontanierii, as one kind of subterranean rodent found in China can survive very low oxygen concentration in labs. It has been demonstrated that long non-coding RNAs (lncRNAs) have important roles in gene expression regulations at different levels and some lncRNAs were found as hypoxia-regulated lncRNAs in cancers. We predicted thousands of lncRNAs in the liver and heart tissues by analyzing RNA-Seq data in Eospalax fontanierii. Those lncRNAs often have shorter lengths, lower expression levels, and lower GC contents than mRNAs. Majors of lncRNAs have expression peaks in hypoxia conditions. We found 1128 DE-lncRNAs (differential expressed lncRNAs) responding to hypoxia. To search the miRNA regulation network for lncRNAs, we predicted 471 and 92 DE-lncRNAs acting as potential miRNA target and target mimics, respectively. We also predicted the functions of DE-lncRNAs based on the co-expression networks of lncRNA-mRNA. The DE-lncRNAs participated in the functions of biological regulation, signaling, development, oxoacid metabolic process, lipid metabolic/biosynthetic process, and catalytic activity. As the first study of lncRNAs in Eospalax fontanierii, our results show that lncRNAs are popular in transcriptome widely and can participate in multiple biological processes in hypoxia responses. MDPI 2021-11-05 /pmc/articles/PMC8929107/ /pubmed/34889903 http://dx.doi.org/10.3390/cimb43030132 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hao, Zhiqiang
Han, Mingfang
Guo, Juanjuan
Li, Guanglin
He, Jianping
Li, Jingang
Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title_full Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title_fullStr Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title_full_unstemmed Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title_short Identification and Functional Analysis of lncRNAs Responsive to Hypoxia in Eospalax fontanierii
title_sort identification and functional analysis of lncrnas responsive to hypoxia in eospalax fontanierii
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8929107/
https://www.ncbi.nlm.nih.gov/pubmed/34889903
http://dx.doi.org/10.3390/cimb43030132
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