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

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.

Pubmed ID: 20436462


  • Guttman M
  • Garber M
  • Levin JZ
  • Donaghey J
  • Robinson J
  • Adiconis X
  • Fan L
  • Koziol MJ
  • Gnirke A
  • Nusbaum C
  • Rinn JL
  • Lander ES
  • Regev A


Nature biotechnology

Publication Data

May 11, 2010

Associated Grants

  • Agency: NIH HHS, Id: DP1 OD003958
  • Agency: NIH HHS, Id: DP1 OD003958-01
  • Agency: NHGRI NIH HHS, Id: R01 HG005111
  • Agency: NHGRI NIH HHS, Id: R01 HG005111-01
  • Agency: Howard Hughes Medical Institute, Id:
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Animals
  • Cell Line
  • Computational Biology
  • DNA, Intergenic
  • Embryonic Stem Cells
  • Gene Expression Profiling
  • Gene Library
  • Mice
  • Models, Genetic
  • RNA, Messenger
  • Sequence Analysis, RNA
  • Transcription, Genetic