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Transcriptome-scale RNase-footprinting of RNA-protein complexes

Ribosome profiling is widely used to study translation in vivo, but not all sequence reads correspond to ribosome-protected RNA. Here, we develop Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, non-ribosomal RNA-protein complexes in the same sample.. We...

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Detalles Bibliográficos
Autores principales: Ji, Zhe, Song, Ruisheng, Huang, Hailiang, Regev, Aviv, Struhl, Kevin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824641/
https://www.ncbi.nlm.nih.gov/pubmed/26900662
http://dx.doi.org/10.1038/nbt.3441
Descripción
Sumario:Ribosome profiling is widely used to study translation in vivo, but not all sequence reads correspond to ribosome-protected RNA. Here, we develop Rfoot, a computational pipeline that analyzes ribosomal profiling data and identifies native, non-ribosomal RNA-protein complexes in the same sample.. We use Rfoot to precisely map RNase-protected regions within small nucleolar RNAs, spliceosomal RNAs, microRNAs, tRNAs, long noncoding (lnc) RNAs, and 3’ˊ 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.