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PLoS Genet. 2014 Apr 17;10(4):e1004288. doi: 10.1371/journal.pgen.1004288. eCollection 2014 Apr.

Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.

Author information

1
Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
2
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada.
3
Wine Research Centre, University of British Columbia, Vancouver, Canada.
4
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
5
Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
6
Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.

Abstract

DNA:RNA hybrid formation is emerging as a significant cause of genome instability in biological systems ranging from bacteria to mammals. Here we describe the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation (DRIP) followed by hybridization on tiling microarray. These profiles show that DNA:RNA hybrids preferentially accumulated at rDNA, Ty1 and Ty2 transposons, telomeric repeat regions and a subset of open reading frames (ORFs). The latter are generally highly transcribed and have high GC content. Interestingly, significant DNA:RNA hybrid enrichment was also detected at genes associated with antisense transcripts. The expression of antisense-associated genes was also significantly altered upon overexpression of RNase H, which degrades the RNA in hybrids. Finally, we uncover mutant-specific differences in the DRIP profiles of a Sen1 helicase mutant, RNase H deletion mutant and Hpr1 THO complex mutant compared to wild type, suggesting different roles for these proteins in DNA:RNA hybrid biology. Our profiles of DNA:RNA hybrid prone loci provide a resource for understanding the properties of hybrid-forming regions in vivo, extend our knowledge of hybrid-mitigating enzymes, and contribute to models of antisense-mediated gene regulation. A summary of this paper was presented at the 26th International Conference on Yeast Genetics and Molecular Biology, August 2013.

PMID:
24743342
PMCID:
PMC3990523
DOI:
10.1371/journal.pgen.1004288
[Indexed for MEDLINE]
Free PMC Article

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