Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

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Summary

A total of 2 542 lincRNAs were identified from Populus trichocarpa and some of them play key roles in drought stress tolerance or regulate microRNA through target mimicry patterns.

Abstract

Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa ( P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis.

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psRNATarget: a plant small RNA target analysis server

Siu-Hong Chan, Xinbin Dai, Patrick Xuechun Zhao (2011)

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/.

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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Y Takenaka, Rodrigo Nakamura, C Bult … (2002)

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

Mitchell Guttman, Manuel Garber, Joshua Levin … (2010)

RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5′-start sites, 3′-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.

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Author and article information

Journal

Journal ID (nlm-ta): J Exp Bot

Journal ID (iso-abbrev): J. Exp. Bot

Journal ID (hwp): jexbot

Journal ID (publisher-id): exbotj

Title: Journal of Experimental Botany

Publisher: Oxford University Press (UK )

ISSN (Print): 0022-0957

ISSN (Electronic): 1460-2431

Publication date (Print): September 2014

Publication date (Electronic): 19 June 2014

Publication date PMC-release: 19 June 2014

Volume: 65

Issue: 17

Pages: 4975-4983

Affiliations

College of Biological Sciences and Technology, National Engineering Laboratory of Tree Breeding, Beijing Forestry University , mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing 100083, P.R. China

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* These authors contributed equally to this work.

^† To whom correspondence should be addressed. E-mail: xiaxl@ 123456bjfu.edu.cn ; yinwl@ 123456bjfu.edu.cn

Article

DOI: 10.1093/jxb/eru256

PMC ID: 4144774

PubMed ID: 24948679

SO-VID: 4c81b620-2368-4b6b-8926-560b04f24315

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

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Climate Change: Open Access

Most cited references 25

psRNATarget: a plant small RNA target analysis server

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

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