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Song, Ruisheng

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Song

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Ruisheng

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Song, Ruisheng

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Author's Publications: search.filters.isAuthorOfPublication.6311502f-3178-4cec-80ac-edf038d12774

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    Transcriptome-scale RNase-footprinting of RNA-protein complexes
    (2015) Ji, Zhe; Song, Ruisheng; Huang, Hailiang; Regev, Aviv; Struhl, Kevin
    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.
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    Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins
    (eLife Sciences Publications, Ltd, 2015) Ji, Zhe; Song, Ruisheng; Regev, Aviv; Struhl, Kevin
    Using a new bioinformatic method to analyze ribosome profiling data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated. In addition, ~35% of mRNA coding genes are translated upstream of the primary protein-coding region (uORFs) and 4% are translated downstream (dORFs). Translated lncRNAs preferentially localize in the cytoplasm, whereas untranslated lncRNAs preferentially localize in the nucleus. The translation efficiency of cytoplasmic lncRNAs is nearly comparable to that of mRNAs, suggesting that cytoplasmic lncRNAs are engaged by the ribosome and translated. While most peptides generated from lncRNAs may be highly unstable byproducts without function, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dORF peptides. Analyses of synonymous and nonsynonymous substitution rates of these conserved peptides show that some are under stabilizing selection, suggesting potential functional importance. DOI: http://dx.doi.org/10.7554/eLife.08890.001