Transcriptome-scale RNase-footprinting of RNA-protein complexes

Zhe Ji, Ruisheng Song, Hailiang Huang, Aviv Regev*, Kevin Struhl

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)410-413
Number of pages4
JournalNature biotechnology
Issue number4
StatePublished - Apr 1 2016

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering


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