Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Mercer, Tim R., Gerhardt, Daniel J., Dinger, Marcel E., Crawford, Joanna, Trapnell, Cole, Jeddeloh, Jeffrey A., Mattick, John S. and Rinn, John L. (2012) Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nature Biotechnology, 30 1: 99-104. doi:10.1038/nbt.2024

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Author Mercer, Tim R.
Gerhardt, Daniel J.
Dinger, Marcel E.
Crawford, Joanna
Trapnell, Cole
Jeddeloh, Jeffrey A.
Mattick, John S.
Rinn, John L.
Title Targeted RNA sequencing reveals the deep complexity of the human transcriptome
Journal name Nature Biotechnology   Check publisher's open access policy
ISSN 1087-0156
Publication date 2012-01-01
Year available 2011
Sub-type Article (original research)
DOI 10.1038/nbt.2024
Open Access Status File (Author Post-print)
Volume 30
Issue 1
Start page 99
End page 104
Total pages 15
Place of publication New York, NY, United States
Publisher Nature Publishing Group
Language eng
Subject 2402 Applied Microbiology and Biotechnology
1305 Biotechnology
1313 Molecular Medicine
1502 Bioengineering
2204 Biomedical Engineering
Abstract Transcriptomic analyses have revealed an unexpected complexity to the human transcriptome, whose breadth and depth exceeds current RNA sequencing capability1, 2, 3, 4. Using tiling arrays to target and sequence select portions of the transcriptome, we identify and characterize unannotated transcripts whose rare or transient expression is below the detection limits of conventional sequencing approaches. We use the unprecedented depth of coverage afforded by this technique to reach the deepest limits of the human transcriptome, exposing widespread, regulated and remarkably complex noncoding transcription in intergenic regions, as well as unannotated exons and splicing patterns in even intensively studied protein-coding loci such as p53 and HOX. The data also show that intermittent sequenced reads observed in conventional RNA sequencing data sets, previously dismissed as noise, are in fact indicative of unassembled rare transcripts. Collectively, these results reveal the range, depth and complexity of a human transcriptome that is far from fully characterized.
Keyword Transcriptomic analyses
Human transcriptome
Tiling arrays
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 13 November 2011.

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Created: Fri, 16 Dec 2011, 21:40:17 EST by Susan Allen on behalf of Institute for Molecular Bioscience