title: Transcriptome-scale RNase-footprinting of RNA-protein complexes.
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.
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.|Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Ji
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Ruisheng
authors.identifier: http://orcid.org/0000-0002-6856-4721
authors.initials: R
authors.lastname: Song
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Analytic and Translation Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
authors.forename: Hailiang
authors.identifier: http://orcid.org/0000-0003-1461-5762
authors.initials: H
authors.lastname: Huang
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Struhl
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D012313:RNA / Q000032:analysis / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA; D012260:Ribonucleases