Transcriptome-scale RNase-footprinting of RNA-protein complexes.

Nat Biotechnol
Authors
Keywords
Abstract

Ribosome profiling is widely used to study translation in vivo, but not all sequence reads correspond to ribosome-protected RNA. Here we describe Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, nonribosomal RNA-protein complexes. We use Rfoot to precisely map RNase-protected regions within small nucleolar RNAs, spliceosomal RNAs, microRNAs, tRNAs, long noncoding (lnc)RNAs and 3' untranslated regions of mRNAs in human cells. We show that RNAs of the same class can show differential complex association. Although only a subset of lncRNAs show RNase footprints, many of these have multiple footprints, and the protected regions are evolutionarily conserved, suggestive of biological functions.

Year of Publication
2016
Journal
Nat Biotechnol
Volume
34
Issue
4
Pages
410-3
Date Published
2016 Apr
ISSN
1546-1696
URL
DOI
10.1038/nbt.3441
PubMed ID
26900662
PubMed Central ID
PMC4824641
Links
Grant list
Howard Hughes Medical Institute / United States
P50 HG006193 / HG / NHGRI NIH HHS / United States
R01 CA107486 / CA / NCI NIH HHS / United States
CA 107486 / CA / NCI NIH HHS / United States