title: The DNA end-binding protein Ku regulates silencing at the internal HML and HMR loci in Saccharomyces cerevisiae.
abstract: Heterochromatin resides near yeast telomeres and at the cryptic mating-type loci, HML and HMR, where it silences transcription of the alpha- and a-mating-type genes, respectively. Ku is a conserved DNA end-binding protein that binds telomeres and regulates silencing in yeast. The role of Ku in silencing is thought to be limited to telomeric silencing. Here, we tested whether Ku contributes to silencing at HML or HMR. Mutant analysis revealed that yKu70 and Sir1 act collectively to silence the mating-type genes at HML and HMR. In addition, loss of yKu70 function leads to expression of different reporter genes inserted at HMR. Quantitative chromatin-immunoprecipitation experiments revealed that yKu70 binds to HML and HMR and that binding of Ku to these internal loci is dependent on Sir4. The interaction between yKu70 and Sir4 was characterized further and found to be dependent on Sir2 but not on Sir1, Sir3, or yKu80. These observations reveal that, in addition to its ability to bind telomeric DNA ends and aid in the silencing of genes at telomeres, Ku binds to internal silent loci via protein-protein interactions and contributes to the efficient silencing of these loci.
authors.affiliation: Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois 61801, USA.
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Vandre
authors.forename: Rohinton T
authors.initials: RT
authors.lastname: Kamakaka
authors.forename: David H
authors.initials: DH
authors.lastname: Rivier
mesh_terms: D047369:Chromatin Immunoprecipitation; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D020868:Gene Silencing; D049770:Genes, Mating Type, Fungal; D016133:Polymerase Chain Reaction; D012441:Saccharomyces cerevisiae / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D016615:Telomere / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae; C520769:YKU70 protein, S cerevisiae; C520770:YKU80 protein, S cerevisiae
references.citation: Mol Cell Biol. 1991 Nov;11(11):5648-59
references.pmid: 1922068
references.citation: Yeast. 1994 Dec;10(13):1793-808
references.pmid: 7747518
references.citation: Nat Rev Genet. 2006 Oct;7(10):793-803
references.pmid: 16983375
references.citation: Curr Opin Cell Biol. 1997 Jun;9(3):383-7
references.pmid: 9159071
references.citation: Cell. 1990 Nov 16;63(4):751-62
references.pmid: 2225075
references.citation: EMBO Rep. 2001 Mar;2(3):197-202
references.pmid: 11266360
references.citation: Yeast. 1999 Jul;15(10B):963-72
references.pmid: 10407276
references.citation: J Biol Chem. 2004 Jan 2;279(1):86-94
references.pmid: 14551211
references.citation: Nat Struct Mol Biol. 2007 Apr;14(4):301-7
references.pmid: 17351632
references.citation: Nucleic Acids Res. 1993 Jul 11;21(14):3329-30
references.pmid: 8341614
references.citation: Curr Opin Cell Biol. 2002 Jun;14(3):377-83
references.pmid: 12067662
references.citation: Cell. 1989 Nov 17;59(4):637-47
references.pmid: 2684414
references.citation: Oncogene. 2002 Jan 21;21(4):512-21
references.pmid: 11850776
references.citation: Nature. 1997 Aug 28;388(6645):900-3
references.pmid: 9278054
references.citation: Annu Rev Genet. 2005;39:431-51
references.pmid: 16285867
references.citation: Genes Dev. 1993 Jul;7(7A):1146-59
references.pmid: 8319907
references.citation: Mol Biol Cell. 2001 Nov;12(11):3386-401
references.pmid: 11694575
references.citation: Cell. 1999 May 28;97(5):621-33
references.pmid: 10367891
references.citation: EMBO J. 2004 Mar 24;23(6):1301-12
references.pmid: 15014445
references.citation: EMBO Rep. 2001 Mar;2(3):203-10
references.pmid: 11266361
references.citation: Genes Dev. 1991 Apr;5(4):616-28
references.pmid: 2010087
references.citation: Curr Biol. 1998 May 21;8(11):657-60
references.pmid: 9635193
references.citation: Proc Natl Acad Sci U S A. 1979 Sep;76(9):4539-43
references.pmid: 388445
references.citation: Nature. 2001 Aug 9;412(6847):607-14
references.pmid: 11493912
references.citation: Annu Rev Biochem. 2007;76:75-100
references.pmid: 17362198
references.citation: Mol Cell. 2005 May 13;18(4):395-8
references.pmid: 15893722
references.citation: DNA Cell Biol. 2003 Feb;22(2):65-78
references.pmid: 12713733
references.citation: Mol Cell Biol. 1993 Jul;13(7):3919-28
references.pmid: 8321199
references.citation: Mol Biol Cell. 1999 Mar;10(3):567-80
references.pmid: 10069804
references.citation: Genes Dev. 1994 Oct 1;8(19):2257-69
references.pmid: 7958893
references.citation: Curr Opin Genet Dev. 2006 Apr;16(2):177-83
references.pmid: 16503127
references.citation: Yeast. 1995 Dec;11(16):1553-73
references.pmid: 8720065
references.citation: Methods Enzymol. 1991;194:3-21
references.pmid: 2005794
references.citation: Curr Biol. 1999 Oct 7;9(19):1123-6
references.pmid: 10531008
references.citation: Cell. 1989 Jun 2;57(5):725-37
references.pmid: 2655930
references.citation: Genetics. 1979 Dec;93(4):877-901
references.pmid: 397913
references.citation: Genetics. 1996 Dec;144(4):1425-36
references.pmid: 8978031
references.citation: Genetics. 2007 Dec;177(4):2541-6
references.pmid: 18073447
references.citation: J Cell Sci. 2008 Mar 1;121(Pt 5):590-600
references.pmid: 18252799
references.citation: Methods Enzymol. 1999;304:414-30
references.pmid: 10372374
references.citation: Science. 1998 May 1;280(5364):741-4
references.pmid: 9563951
references.citation: Biochim Biophys Acta. 2004 Mar 15;1677(1-3):120-8
references.pmid: 15020053
references.citation: Genes Dev. 2003 Oct 1;17(19):2347-50
references.pmid: 14522942
references.citation: J Cell Sci. 2005 Aug 1;118(Pt 15):3247-61
references.pmid: 16014376
references.citation: Genetics. 1999 Sep;153(1):13-23
references.pmid: 10471696
references.citation: Cell. 1985 May;41(1):41-8
references.pmid: 3888409
references.citation: Genetics. 2008 Oct;180(2):771-83
references.pmid: 18716325
references.citation: Genetics. 1999 Feb;151(2):521-9
references.pmid: 9927448
references.citation: Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):867-72
references.pmid: 9023348
references.citation: Yeast. 1999 Aug;15(11):1141-9
references.pmid: 10455237
references.citation: BMC Mol Biol. 2006 Dec 22;7:48
references.pmid: 17187679
references.citation: Cell. 1987 Dec 4;51(5):721-32
references.pmid: 3315231
references.citation: Nat Rev Mol Cell Biol. 2006 Sep;7(9):657-66
references.pmid: 16912715
references.citation: DNA Repair (Amst). 2005 Nov 21;4(11):1215-26
references.pmid: 15979949
references.citation: Mol Cell Biol. 1988 Jan;8(1):210-25
references.pmid: 3275867
references.citation: Yeast. 1991 Apr;7(3):253-63
references.pmid: 1882550
references.citation: EMBO J. 1998 Mar 16;17(6):1819-28
references.pmid: 9501103
references.citation: Yeast. 1999 Oct;15(14):1541-53
references.pmid: 10514571
references.citation: Nucleic Acids Res. 2007;35(7):2302-10
references.pmid: 17389650
references.citation: Mol Cell Biol. 2008 Mar;28(6):1924-35
references.pmid: 18195043
references.citation: Mol Cell Biol. 1989 Nov;9(11):4621-30
references.pmid: 2689860
references.citation: Trends Genet. 1994 Nov;10(11):408-12
references.pmid: 7809947
references.citation: Genetics. 1979 Sep;93(1):13-35
references.pmid: 16118901
references.citation: Cell. 2004 Dec 29;119(7):955-67
references.pmid: 15620354
references.citation: Curr Genet. 1989 Oct;16(4):225-39
references.pmid: 2697465
references.citation: Annu Rev Cell Dev Biol. 1995;11:519-48
references.pmid: 8689568
references.citation: Annu Rev Biochem. 2003;72:481-516
references.pmid: 12676793
references.citation: Curr Biol. 1998 May 21;8(11):653-6
references.pmid: 9635192