Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
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Author(s)
Guttman, Mitchell
Garber, Manuel
Levin, Joshua Z.
Donaghey, Julie
Robinson, James
Adiconis, Xian
Fan, Lin
Koziol, Magdalena J.
Gnirke, Andreas
Nusbaum, Chad
Alternative Title
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Date Issued
July 2010
Journal
Nature Biotechnology
Publisher
Nature Publishing Group
Citation
Guttman, Mitchell et al. “Ab Initio Reconstruction of Cell Type–specific Transcriptomes in Mouse Reveals the Conserved Multi-exonic Structure of lincRNAs.” Nature Biotechnology 28.5 (2010): 503–510. Web.
Version
Author's final manuscript
Abstract
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.
Description
available in PMC 2010 November 2.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution-Noncommercial-Share Alike 3.0
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DOI of Published Version
https://doi.org/10.1038/nbt.1633
