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Bioinformatics. 2012 Nov 1;28(21):2719-23. doi: 10.1093/bioinformatics/bts534. Epub 2012 Aug 31.

Antisense transcription is coupled to nucleosome occupancy in sense promoters.

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Department of Electronics, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou 510006, China.



Genome-wide pervasive transcription is widespread in eukaryotes, revealing an extensive array of antisense transcription that involves hundreds of previously unknown non-coding RNAs. Individual cases have shown that antisense transcription influences sense transcription, however, genome-wide mechanisms of how antisense transcription regulates sense transcription remain to be elucidated.


Here, we performed a systematic analysis of sense-antisense transcription and nucleosome occupancy in yeast. We found that antisense transcription is associated with nucleosome occupancy in sense promoters. Using RNA polymerase II inactivation data as a reasonable approximation to antisense transcription inactivation data, we further showed that antisense transcripts increase nucleosome occupancy in sense promoter regions they overlap, and reduce nucleosome occupancy in sense promoter regions around their transcription termination sites. These results reveal the previously unappreciated roles of antisense transcription in directing nucleosome occupancy in sense promoters. Our findings will have implications in understanding regulatory functions of antisense transcription.

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