title: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.
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.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. mguttman@mit.edu
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
authors.forename: Manuel
authors.initials: M
authors.lastname: Garber
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Julie
authors.initials: J
authors.lastname: Donaghey
authors.forename: James
authors.initials: J
authors.lastname: Robinson
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.forename: Magdalena J
authors.initials: MJ
authors.lastname: Koziol
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D021901:DNA, Intergenic / Q000235:genetics*; D053595:Embryonic Stem Cells; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D051379:Mice; D008957:Models, Genetic; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D012333:RNA, Messenger