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Nat Biotechnol. 2010 May;28(5):503-10. doi: 10.1038/nbt.1633. Epub 2010 May 2.

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

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  • 1Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. mguttman@mit.edu

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  • Nat Biotechnol. 2010 Jul;28(7):756.

Abstract

Massively parallel cDNA sequencing (RNA-Seq) provides an unbiased way to study a transcriptome, including both coding and noncoding genes. Until now, most RNA-Seq studies have depended crucially 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 applied it to mouse embryonic stem cells, neuronal precursor cells and lung fibroblasts to accurately reconstruct the full-length gene structures for most known expressed genes. We identified substantial variation in protein coding genes, including thousands of novel 5' start sites, 3' ends and internal coding exons. We then determined the gene structures of more than a thousand large intergenic noncoding RNA (lincRNA) and antisense loci. Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes.

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PMID:
20436462
[PubMed - indexed for MEDLINE]
PMCID:
PMC2868100
Free PMC Article

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