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


Computational analysis for Structure-seq (red), dimethyl sulfate sequencing (DMS-seq; cyan) and modification sequencing (Mod-seq; purple). Raw reads are treated similarly in the initial steps, including reads mapping and calculation of reverse transcription (RT) stop counts on each nucleotide (in gray boxes).

  • Transcriptome-wide RNA structure probing coupled with NGS yields the RNA structurome.
  • RNA structurome data tremendously improve prediction of in vivo RNA structure.
  • RNA structurome data uncover relationships between RNA structure and gene regulation.

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.

Kwok CK, Tang Y, Assmann SM, Bevilacqua PC. (2015) The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends in Biochemical Sciences. [epub ahead of print]. [abstract]

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