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Transcriptome-wide investigation of circular RNAs in rice

Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and t...

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Autores principales: Lu, Tingting, Cui, Lingling, Zhou, Yan, Zhu, Chuanrang, Fan, Danlin, Gong, Hao, Zhao, Qiang, Zhou, Congcong, Zhao, Yan, Lu, Danfeng, Luo, Jianghong, Wang, Yongchun, Tian, Qilin, Feng, Qi, Huang, Tao, Han, Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647462/
https://www.ncbi.nlm.nih.gov/pubmed/26464523
http://dx.doi.org/10.1261/rna.052282.115
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author Lu, Tingting
Cui, Lingling
Zhou, Yan
Zhu, Chuanrang
Fan, Danlin
Gong, Hao
Zhao, Qiang
Zhou, Congcong
Zhao, Yan
Lu, Danfeng
Luo, Jianghong
Wang, Yongchun
Tian, Qilin
Feng, Qi
Huang, Tao
Han, Bin
author_facet Lu, Tingting
Cui, Lingling
Zhou, Yan
Zhu, Chuanrang
Fan, Danlin
Gong, Hao
Zhao, Qiang
Zhou, Congcong
Zhao, Yan
Lu, Danfeng
Luo, Jianghong
Wang, Yongchun
Tian, Qilin
Feng, Qi
Huang, Tao
Han, Bin
author_sort Lu, Tingting
collection PubMed
description Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs.
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spelling pubmed-46474622015-12-01 Transcriptome-wide investigation of circular RNAs in rice Lu, Tingting Cui, Lingling Zhou, Yan Zhu, Chuanrang Fan, Danlin Gong, Hao Zhao, Qiang Zhou, Congcong Zhao, Yan Lu, Danfeng Luo, Jianghong Wang, Yongchun Tian, Qilin Feng, Qi Huang, Tao Han, Bin RNA Article Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs. Cold Spring Harbor Laboratory Press 2015-12 /pmc/articles/PMC4647462/ /pubmed/26464523 http://dx.doi.org/10.1261/rna.052282.115 Text en © 2015 Lu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Lu, Tingting
Cui, Lingling
Zhou, Yan
Zhu, Chuanrang
Fan, Danlin
Gong, Hao
Zhao, Qiang
Zhou, Congcong
Zhao, Yan
Lu, Danfeng
Luo, Jianghong
Wang, Yongchun
Tian, Qilin
Feng, Qi
Huang, Tao
Han, Bin
Transcriptome-wide investigation of circular RNAs in rice
title Transcriptome-wide investigation of circular RNAs in rice
title_full Transcriptome-wide investigation of circular RNAs in rice
title_fullStr Transcriptome-wide investigation of circular RNAs in rice
title_full_unstemmed Transcriptome-wide investigation of circular RNAs in rice
title_short Transcriptome-wide investigation of circular RNAs in rice
title_sort transcriptome-wide investigation of circular rnas in rice
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647462/
https://www.ncbi.nlm.nih.gov/pubmed/26464523
http://dx.doi.org/10.1261/rna.052282.115
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