NDLI: Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Liu, Jun Jung, Choonkyun Xu, Jun Wang, Huan Deng, Shulin Bernad, Lucia Arenas-Huertero, Catalina Chua, Nam-Hai
Description	Country affiliation: United States Author Affiliation: Liu J ( Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065, USA.)
Abstract	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 by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of intron-containing lincRNAs.
File Format	HTM / HTML
ISSN	10404651
e-ISSN	1531298X
DOI	10.1105/tpc.112.102855
Journal	THE PLANT CELL ONLINE
Issue Number	11
Volume Number	24
Language	English
Publisher	American Society of Plant Biologists
Publisher Date	2012-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Botany Arabidopsis Proteins Genetics Arabidopsis Calcium-binding Proteins Gene Expression Regulation, Plant Intercellular Signaling Peptides And Proteins Membrane Proteins Rna, Long Noncoding Rna-binding Proteins Metabolism Computational Biology Gene Expression Profiling Gene Library Introns Mutation Oligonucleotide Array Sequence Analysis Organ Specificity Plant Roots Rna Splicing Rna, Plant Sequence Analysis, Rna Stress, Physiological Transcriptome Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Cell Biology Plant Science

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