The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

Chun Kit Kwok; Yin Tang; Sarah M Assmann; Philip C Bevilacqua

doi:10.1016/j.tibs.2015.02.005

The RNA structurome: transcriptome-wide structure probing with next-generation sequencing

Trends Biochem Sci. 2015 Apr;40(4):221-32. doi: 10.1016/j.tibs.2015.02.005. Epub 2015 Mar 18.

Authors

Chun Kit Kwok¹, Yin Tang², Sarah M Assmann³, Philip C Bevilacqua⁴

Affiliations

¹ Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: ckk26@cam.ac.uk.
² Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA.
³ Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA; Plant Biology Graduate Program, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: sma3@psu.edu.
⁴ Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Plant Biology Graduate Program, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: pcb5@psu.edu.

PMID: 25797096
DOI: 10.1016/j.tibs.2015.02.005

Abstract

RNA folds into intricate structures that enable its pivotal roles in biology, ranging from regulation of gene expression to ligand sensing and enzymatic functions. Therefore, elucidating RNA structure can provide profound insights into living systems. A recent marriage between in vivo RNA structure probing and next-generation sequencing (NGS) has revolutionized the RNA field by enabling transcriptome-wide structure determination in vivo, which has been applied to date to human cells, yeast cells, and Arabidopsis seedlings. Analysis of resultant in vivo 'RNA structuromes' provides new and important information regarding myriad cellular processes, including control of translation, alternative splicing, alternative polyadenylation, energy-dependent unfolding of mRNA, and effects of proteins on RNA structure. An emerging view suggests potential links between RNA structure and stress and disease physiology across the tree of life. As we discuss here, these exciting findings open new frontiers into RNA biology, genome biology, and beyond.

Keywords: RNA structure; RNA structurome; next-generation sequencing (NGS); structure prediction; structure probing; transcriptome.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

High-Throughput Nucleotide Sequencing / methods*
Humans
Nucleic Acid Conformation
RNA / genetics*
Transcriptome / genetics*

Substances

RNA