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Identification of long ncRNAs using RNA-seq in Arabidopsis

ABSTRACT: We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq. Transcriptom profiling in roots, leaves, flowers and siliques.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jun Liu

PROVIDER: E-GEOD-38612 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis.

Liu Jun J Jung Choonkyun C Xu Jun J Wang Huan H Deng Shulin S Bernad Lucia L Arenas-Huertero Catalina C Chua Nam-Hai NH

The Plant cell 20121106 11

Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected ...[more]

PMID: 23136377

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