title: Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis.
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.
authors.affiliation: Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY 10065, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Choonkyun
authors.initials: C
authors.lastname: Jung
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.forename: Huan
authors.initials: H
authors.lastname: Wang
authors.forename: Shulin
authors.initials: S
authors.lastname: Deng
authors.forename: Lucia
authors.initials: L
authors.lastname: Bernad
authors.forename: Catalina
authors.initials: C
authors.lastname: Arenas-Huertero
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics*; D002135:Calcium-Binding Proteins / Q000235:genetics*; D019295:Computational Biology; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics*; D007438:Introns; D008565:Membrane Proteins / Q000235:genetics*; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D012326:RNA Splicing; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA; D000072099:Serrate-Jagged Proteins; D013312:Stress, Physiological; D059467:Transcriptome; D039381:RNA Cap-Binding Proteins
chemical_list: D029681:Arabidopsis Proteins; D002135:Calcium-Binding Proteins; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D062085:RNA, Long Noncoding; D018749:RNA, Plant; D016601:RNA-Binding Proteins; D000072099:Serrate-Jagged Proteins; C454128:CBP20 protein, Arabidopsis; C000606277:SE protein, Arabidopsis; C435105:At2g13540 protein, Arabidopsis; D039381:RNA Cap-Binding Proteins