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Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computationa...

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Autores principales: Xu, Xi-Wen, Zhou, Xiong-Hui, Wang, Rui-Ru, Peng, Wen-Lei, An, Yue, Chen, Ling-Ling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748279/
https://www.ncbi.nlm.nih.gov/pubmed/26860696
http://dx.doi.org/10.1038/srep20715
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author Xu, Xi-Wen
Zhou, Xiong-Hui
Wang, Rui-Ru
Peng, Wen-Lei
An, Yue
Chen, Ling-Ling
author_facet Xu, Xi-Wen
Zhou, Xiong-Hui
Wang, Rui-Ru
Peng, Wen-Lei
An, Yue
Chen, Ling-Ling
author_sort Xu, Xi-Wen
collection PubMed
description Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation.
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spelling pubmed-47482792016-02-17 Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network Xu, Xi-Wen Zhou, Xiong-Hui Wang, Rui-Ru Peng, Wen-Lei An, Yue Chen, Ling-Ling Sci Rep Article Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation. Nature Publishing Group 2016-02-10 /pmc/articles/PMC4748279/ /pubmed/26860696 http://dx.doi.org/10.1038/srep20715 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Xu, Xi-Wen
Zhou, Xiong-Hui
Wang, Rui-Ru
Peng, Wen-Lei
An, Yue
Chen, Ling-Ling
Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title_full Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title_fullStr Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title_full_unstemmed Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title_short Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
title_sort functional analysis of long intergenic non-coding rnas in phosphate-starved rice using competing endogenous rna network
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748279/
https://www.ncbi.nlm.nih.gov/pubmed/26860696
http://dx.doi.org/10.1038/srep20715
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