title: Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.
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.
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
authors.forename: Yujia A
authors.initials: YA
authors.lastname: Chan
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Aristizabal
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada.
authors.forename: Phoebe Y T
authors.initials: PY
authors.lastname: Lu
authors.affiliation: Wine Research Centre, University of British Columbia, Vancouver, Canada.
authors.forename: Zongli
authors.initials: Z
authors.lastname: Luo
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.
authors.forename: Akil
authors.initials: A
authors.lastname: Hamza
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Kobor
authors.affiliation: Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
authors.forename: Peter C
authors.initials: PC
authors.lastname: Stirling
authors.affiliation: Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Philip
authors.initials: P
authors.lastname: Hieter
mesh_terms: D016375:Antisense Elements (Genetics) / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D047468:Immunoprecipitation / Q000379:methods; D009687:Nuclear Proteins / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016366:Open Reading Frames / Q000235:genetics; D012331:RNA, Fungal / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D016914:Ribonuclease H / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D017384:Sequence Deletion / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D016375:Antisense Elements (Genetics); D004271:DNA, Fungal; D004275:DNA, Ribosomal; C063494:HPR1 protein, S cerevisiae; D009687:Nuclear Proteins; D012331:RNA, Fungal; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D016914:Ribonuclease H; D004265:DNA Helicases
references.citation: Genes Dev. 2008 Apr 15;22(8):1082-92
references.pmid: 18413718
references.citation: Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15657-62
references.pmid: 19721006
references.citation: PLoS Genet. 2012 Sep;8(9):e1002952
references.pmid: 23028359
references.citation: EMBO J. 1997 Oct 15;16(20):6272-80
references.pmid: 9321406
references.citation: Mol Cell. 2010 Jun 11;38(5):675-88
references.pmid: 20542000
references.citation: Mol Cell. 2011 Dec 23;44(6):966-77
references.pmid: 22195969
references.citation: Mol Cell. 2012 Mar 30;45(6):814-25
references.pmid: 22387027
references.citation: Nucleic Acids Res. 2008 Mar;36(4):e21
references.pmid: 18180247
references.citation: Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):13938-43
references.pmid: 23918391
references.citation: Mol Cell. 2013 Jun 6;50(5):611-2
references.pmid: 23746348
references.citation: Mol Cell. 2012 Nov 9;48(3):365-74
references.pmid: 23041286
references.citation: Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):258-63
references.pmid: 23251031
references.citation: Genes Dev. 2009 Jul 1;23(13):1534-45
references.pmid: 19571181
references.citation: Cell. 2011 Mar 4;144(5):646-74
references.pmid: 21376230
references.citation: N Engl J Med. 2011 Dec 29;365(26):2497-506
references.pmid: 22150006
references.citation: Science. 2013 May 3;340(6132):619-21
references.pmid: 23641115
references.citation: Genes Dev. 2012 Jan 15;26(2):163-75
references.pmid: 22279048
references.citation: J Cell Biol. 1992 Jun;117(5):935-48
references.pmid: 1315786
references.citation: Mol Cell Biol. 2001 Oct;21(20):7054-64
references.pmid: 11564888
references.citation: Nature. 2003 Apr 17;422(6933):726-30
references.pmid: 12692563
references.citation: Mol Cell. 2009 Oct 9;36(1):88-98
references.pmid: 19818712
references.citation: Mol Syst Biol. 2011 Feb 15;7:468
references.pmid: 21326235
references.citation: Nucleic Acids Res. 1997 Dec 1;25(23):4778-85
references.pmid: 9365256
references.citation: N Engl J Med. 2011 Oct 13;365(15):1384-95
references.pmid: 21995386
references.citation: Nucleic Acids Res. 2006 Apr 13;34(7):e52
references.pmid: 16614443
references.citation: Mol Cell. 2011 Jun 24;42(6):794-805
references.pmid: 21700224
references.citation: PLoS One. 2013 Jun 07;8(6):e65541
references.pmid: 23762389
references.citation: Nat Rev Mol Cell Biol. 2009 Sep;10(9):637-43
references.pmid: 19638999
references.citation: Nucleic Acids Res. 1996 Jun 15;24(12):2338-46
references.pmid: 8710505
references.citation: EMBO J. 2002 Jul 1;21(13):3526-35
references.pmid: 12093753
references.citation: EMBO J. 2013 Oct 30;32(21):2861-71
references.pmid: 24084588
references.citation: DNA Repair (Amst). 2012 Dec 1;11(12):933-41
references.pmid: 23079308
references.citation: Genes Dev. 2013 Nov 15;27(22):2445-58
references.pmid: 24240235
references.citation: Bioinformatics. 2012 Mar 1;28(5):717-8
references.pmid: 22238257
references.citation: Mol Cell. 2003 Sep;12(3):711-21
references.pmid: 14527416
references.citation: J Biol Chem. 1988 Jan 25;263(3):1413-23
references.pmid: 2447089
references.citation: Cell. 1997 Oct 3;91(1):35-45
references.pmid: 9335333
references.citation: EMBO Rep. 2012 Oct;13(10):923-9
references.pmid: 22878416
references.citation: Mol Cell. 2009 Sep 11;35(5):626-41
references.pmid: 19682934
references.citation: Genome Res. 2013 Oct;23(10):1590-600
references.pmid: 23868195
references.citation: Nucleic Acids Res. 2012 Jul;40(12):5271-82
references.pmid: 22379133
references.citation: Mol Biol Cell. 2008 Oct;19(10):4310-8
references.pmid: 18667528
references.citation: Mol Cell. 2012 Apr 27;46(2):115-24
references.pmid: 22541554
references.citation: Nat Struct Mol Biol. 2013 Jul;20(7):851-8
references.pmid: 23770821
references.citation: PLoS Genet. 2011 Dec;7(12):e1002386
references.pmid: 22144908
references.citation: EMBO J. 2011 Jun 24;30(15):3106-19
references.pmid: 21701562
references.citation: Mol Cell. 2006 Dec 8;24(5):735-746
references.pmid: 17157256
references.citation: Genome Biol. 2010;11(8):R87
references.pmid: 20796282
references.citation: Nature. 2002 May 16;417(6886):304-8
references.pmid: 11979277
references.citation: Genes Dev. 2010 Jul 15;24(14):1546-58
references.pmid: 20634320
references.citation: Cell. 1998 Nov 25;95(5):717-28
references.pmid: 9845373
references.citation: Mol Cell. 2011 Dec 23;44(6):978-88
references.pmid: 22195970
references.citation: Genes Dev. 2011 Oct 1;25(19):2041-56
references.pmid: 21979917
references.citation: Mol Cell. 2005 Jun 10;18(6):711-22
references.pmid: 15949445
references.citation: PLoS Genet. 2013 Aug;9(8):e1003758
references.pmid: 24009531
references.citation: Genes Cells. 2012 Mar;17(3):218-33
references.pmid: 22280061
references.citation: Cell. 2013 Mar 28;153(1):17-37
references.pmid: 23540688
references.citation: Cancer Res. 2012 Apr 15;72(8):2111-9
references.pmid: 22354749
references.citation: Nature. 2008 Jul 3;454(7200):126-30
references.pmid: 18509338
references.citation: Cell. 2012 Nov 9;151(4):835-846
references.pmid: 23141540
references.citation: Nucleic Acids Res. 2013 Dec;41(22):10110-23
references.pmid: 23999093
references.citation: Nature. 2011 Jun 22;475(7354):114-7
references.pmid: 21697827
references.citation: Mol Cell. 2008 Nov 21;32(4):465-77
references.pmid: 19026778
references.citation: Hum Mol Genet. 2009 Sep 15;18(18):3384-96
references.pmid: 19515850
references.citation: Cell. 2005 Aug 12;122(3):365-78
references.pmid: 16096057
references.citation: Mol Cell Biol. 2002 Dec;22(23):8241-53
references.pmid: 12417727
references.citation: Nat Genet. 2006 Aug;38(8):910-6
references.pmid: 16845400
references.citation: PLoS Genet. 2008 Dec;4(12):e1000290
references.pmid: 19057669
references.citation: J Immunol Methods. 1986 May 1;89(1):123-30
references.pmid: 2422282
references.citation: Mol Cell. 2011 Jan 7;41(1):21-32
references.pmid: 21211720
references.citation: Genetics. 2010 Jul;185(3):1111-28
references.pmid: 20439772
references.citation: Elife. 2013 Jun 11;2:e00505
references.pmid: 23795288
references.citation: Nat Struct Mol Biol. 2013 Oct;20(10):1199-205
references.pmid: 24013207
references.citation: Cold Spring Harb Symp Quant Biol. 2010;75:357-64
references.pmid: 21502405
references.citation: J Biol Chem. 2003 Jun 27;278(26):24225-32
references.pmid: 12702719
references.citation: PLoS Genet. 2011 Apr;7(4):e1002057
references.pmid: 21552543
references.citation: Database (Oxford). 2011 Jul 23;2011:bar030
references.pmid: 21785142