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|a Guttman, Mitchell
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|a Massachusetts Institute of Technology. Department of Biology
|e contributor
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|a Guttman, Mitchell
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|a Lander, Eric S.
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|a Regev, Aviv
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|a Garber, Manuel
|e author
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|a Levin, Joshua Z.
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|a Donaghey, Julie
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|a Robinson, James
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|a Adiconis, Xian
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|a Fan, Lin
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|a Koziol, Magdalena J.
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|a Gnirke, Andreas
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|a Nusbaum, Chad
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|a Rinn, John L.
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|a Regev, Aviv
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|a Lander, Eric Steven
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|a Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
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|a Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
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|b Nature Publishing Group,
|c 2012-10-12T18:54:20Z.
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|z Get fulltext
|u http://hdl.handle.net/1721.1/73946
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|a available in PMC 2010 November 2.
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|a RNA-Seq provides an unbiased way to study a transcriptome, including both coding and noncoding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5'-start sites, 3'-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.
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|a Merkin Family Foundation for Stem Cell Research
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|a Howard Hughes Medical Institute
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|a National Human Genome Research Institute (U.S.)
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|a Burroughs Wellcome Fund
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|a Broad Institute
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|a en_US
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|a Article
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|t Nature Biotechnology
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