NDLI: Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Li, Fan Zheng, Qi Vandivier, Lee E. Willmann, Matthew R. Chen, Ying Gregory, Brian D.
Description	Country affiliation: United States Author Affiliation: Li F ( Department of Biology, University of Pensylvania, Philadelphia, Pensylvania 19104, USA.)
Abstract	The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.
File Format	HTM / HTML
ISSN	10404651
e-ISSN	1531298X
DOI	10.1105/tpc.112.104232
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 Genetics Gene Expression Regulation, Plant Genome, Plant Nucleic Acid Conformation Rna, Plant Transcriptome Gene Library High-throughput Nucleotide Sequencing Micrornas Models, Molecular Rna Folding Rna, Messenger Sequence Analysis, Rna Research Support, N.i.h., Extramural Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Cell Biology Plant Science

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