Jul 3, 2014

Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells

BioRxiv : the Preprint Server for Biology
Corey T WatsonFelix Breden

Abstract

RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.

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Mentioned in this Paper

Bacitracin
Genome
Genes
Segmental Duplications, Genomic
Pathogenic Organism
Gene Conversion of Immunoglobulin Genes
SLC3A2 gene
Nucleic Acid Sequencing
Indusium Griseum
LECT1 gene

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