Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

• Main Authors: Guttman, Mitchell (Contributor), Garber, Manuel (Author), Levin, Joshua Z. (Author), Donaghey, Julie (Author), Robinson, James (Author), Adiconis, Xian (Author), Fan, Lin (Author), Koziol, Magdalena J. (Author), Gnirke, Andreas (Author), Nusbaum, Chad (Author), Rinn, John L. (Author), Regev, Aviv (Contributor), Lander, Eric Steven (Author)
• Other Authors: Massachusetts Institute of Technology. Department of Biology (Contributor), Lander, Eric S. (Contributor)
• Format: Article
• Language: English
• Published: Nature Publishing Group, 2012-10-12T18:54:20Z.
• Subjects: Article
• Online Access: Get fulltext

available in PMC 2010 November 2.
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.
Merkin Family Foundation for Stem Cell Research
Howard Hughes Medical Institute
National Human Genome Research Institute (U.S.)
Burroughs Wellcome Fund
Broad Institute