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Published Online December 4, 2008
Science DOI: 10.1126/science.1163853

Reports

Submitted on July 26, 2008
Accepted on November 10, 2008

The Antisense Transcriptomes of Human Cells

Yiping He 1, Bert Vogelstein 1, Victor E. Velculescu 1, Nickolas Papadopoulos 1*, Kenneth W. Kinzler 1

1 Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.

* To whom correspondence should be addressed.
Nickolas Papadopoulos , E-mail: npapado1{at}jhmi.edu

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the plus- or minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here, we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.


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