Transcriptome-scale RNase-footprinting of RNA-protein complexes
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Regev_Transcription-scale.pdf
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Author(s)
Ji, Zhe
Song, Ruisheng
Huang, Hailiang
Regev, Aviv
Struhl, Kevin
Date Issued
February 2016
Journal
Nature Biotechnology
Publisher
Nature Publishing Group
Citation
Ji, Zhe et al. “Transcriptome-Scale RNase-Footprinting of RNA-Protein Complexes.” Nature Biotechnology 34.4 (2016): 410–413.
Version
Author's final manuscript
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.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution-Noncommercial-Share Alike
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DOI of Published Version
https://doi.org/10.1038/nbt.3441
