Epistatic Interaction Between the K-Homology Domain Protein HEK2 and SIR1 at HMR and Telomeres in Yeast

Journal of Molecular Biology

Volumn 375, Issue 4, 2008, Pages 1178-1187

  Denisenko, Oleg ^a   Bomsztyk, Karol ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Gene silencing; Hek2; HMR; Sir proteins; Telomeres

Indexed keywords

GENE PRODUCT; PROTEIN HEK2; PROTEIN HEK2P; PROTEIN HMR; PROTEIN SIR1; PROTEIN SIR3P; SILENT INFORMATION REGULATOR PROTEIN 2; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA MICROARRAY; EPISTASIS; GENE LOCUS; GENE MUTATION; GENE SILENCING; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; HEK2 GENE; HMR GENE; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REGULATORY MECHANISM; SIR1 GENE; TELOMERE; YEAST;

SACCHAROMYCETALES;

EID: 37449025119     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.11.001     Document Type: Article

References (53)

1. van Holde K. Chromatin (1988), Springer-Verlag, Berlin, Germany
2. Aparicio O.M., Billington B.L., and Gottschling D.E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66 (1991) 1279-1287
3. Vega-Palas M.A., Venditti S., and Di Mauro E. Telomeric transcriptional silencing in a natural context. Nat. Genet. 15 (1997) 232-233
4. Rusche L.N., Kirchmaier A.L., and Rine J. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72 (2003) 481-516
5. Venditti S., Vega-Palas M.A., and Di Mauro E. Heterochromatin organization of a natural yeast telomere. Recruitment of Sir3p through interaction with histone H4 N terminus is required for the establishment of repressive structures. J. Biol. Chem. 274 (1999) 1928-1933
6. Carmen A.A., Milne L., and Grunstein M. Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem. 277 (2002) 4778-4781
7. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 (2001) 120-124
8. Lachner M., O'Carroll D., Rea S., Mechtler K., and Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410 (2001) 116-120
9. Kimura A., Umehara T., and Horikoshi M. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat. Genet. 32 (2002) 370-377
10. Suka N., Luo K., and Grunstein M. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine 16 and spreading of heterochromatin. Nat. Genet. 32 (2002) 378-383
11. Jenuwein T., and Allis C.D. Translating the histone code. Science 293 (2001) 1074-1080
12. Turner B.M. Cellular memory and the histone code. Cell 111 (2002) 285-291
13. Cortes A., Huertas D., Fanti L., Pimpinelli S., Marsellach F.X., Pina B., and Azorin F. DDP1, a single-stranded nucleic acid-binding protein of Drosophila, associates with pericentric heterochromatin and is functionally homologous to the yeast Scp160p, which is involved in the control of cell ploidy. EMBO J. 18 (1999) 3820-3833
14. Konkel L.M.C., Enomoto S., Chamberlain E.M., McCune-Zierath P., Iyadurau S.J.P., and Berman J. A class of single-stranded telomeric DNA-binding proteins required for Rap1p localization in yeast nuclei. Proc. Natl Acad. Sci. USA 92 (1995) 5558-5562
15. LaBranche H., Dupuis S., Ben-David Y., Bani M.R., Wellinger R.J., and Chabot B. Telomere elongation by hnRNP A1 and a derivative that interacts with telomeric repeats and telomerase [see comments]. Nat. Genet. 19 (1998) 199-202
16. Denisenko O.N., and Bomsztyk K. The product of the murine homolog of the Drosophila extra sex comb gene displays transcriptional repressor activity. Mol. Cell. Biol. 17 (1997) 4707-4717
17. Denisenko O., and Bomsztyk K. Yeast hnRNP K-like genes are involved in regulation of the telomeric position effect and telomere length. Mol. Cell. Biol. 22 (2002) 286-297
18. Huertas D., Cortes A., Casanova J., and Azorin F. Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation. Curr. Biol. 14 (2004) 1611-1620
19. Burd C.G., and Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science 265 (1994) 615-621
20. Bomsztyk K., Denisenko O., and Ostrowski J. hnRNP K: one protein multiple processes. BioEssays 26 (2004) 629-638
21. Michelotti E.F., Michelotti G.A., Aronsohn A.I., and Levens D. Heterogeneous nuclear ribonucleoprotein K is a transcription factor. Mol. Cell. Biol. 16 (1996) 2350-2360
22. Ostrowski J., Kawata Y., Schullery D.S., Denisenko O.N., and Bomsztyk K. Transient recruitment of the hnRNP K protein to inducibly transcribed gene loci. Nucleic Acids Res. 31 (2003) 3954-3962
23. Shnyreva M., Schullery D.S., Suzuki H., Higaki Y., and Bomsztyk K. Interaction of two multifunctional proteins. Heterogeneous nuclear ribonucleoprotein K and Y-box-binding protein. J. Biol. Chem. 275 (2000) 15498-15503
24. Marsellach F.X., Huertas D., and Azorin F. The multi-KH domain protein of Saccharomyces cerevisiae Scp160p contributes to the regulation of telomeric silencing. J. Biol. Chem. 281 (2006) 18227-18235
25. Renauld H., Aparicio O.M., Zierath P.D., Billington B.L., Chhablani S.K., and Gottschling D.E. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 7 (1993) 1133-1145
26. Boeke J.D., Trueheart J., Natsoulis G., and Fink G.R. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154 (1987) 164-175
27. Pillus L., and Rine J. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell 59 (1989) 637-647
28. Rine J., Strathern J.N., Hicks J.B., and Herskowitz I. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Genetics 93 (1979) 877-901
29. Gardner K.A., and Fox C.A. The Sir1 protein's association with a silenced chromosome domain. Genes Dev. 15 (2001) 147-157
30. Pryde F.E., and Louis E.J. Limitations of silencing at native yeast telomeres. EMBO J. 18 (1999) 2538-2550
31. Nelson J.D., Denisenko O., and Bomsztyk K. Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nature Protocols 1 (2006) 179-185
32. Kuo M.H., and Allis C.D. In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 19 (1999) 425-433
33. Rusche L.N., Kirchmaier A.L., and Rine J. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13 (2002) 2207-2222
34. Rine J., and Herskowitz I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116 (1987) 9-22
35. Singer M.S., Kahana A., Wolf A.J., Meisinger L.L., Peterson S.E., Goggin C., et al. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150 (1998) 613-632
36. Ng H.H., Robert F., Young R.A., and Struhl K. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev. 16 (2002) 806-819
37. Fourel G., Revardel E., Koering C.E., and Gilson E. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 18 (1999) 2522-2537
38. Fourel G., Lebrun E., and Gilson E. Protosilencers as building blocks for heterochromatin. BioEssays 24 (2002) 828-835
39. Vannier D., Balderes D., and Shore D. Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics 144 (1996) 1343-1353
40. Sun Z.W., and Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152 (1999) 921-932
41. Smith J.S., Caputo E., and Boeke J.D. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19 (1999) 3184-3197
42. Askree S.H., Yehuda T., Smolikov S., Gurevich R., Hawk J., Coker C., et al. A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc. Natl. Acad. Sci. USA 101 (2004) 8658-8663
43. Denisenko O., Shnyreva M., Suzuki H., and Bomsztyk K. Point mutations in the WD40 domain of Eed block its interaction with Ezh2. Mol. Cell. Biol. 18 (1998) 5634-5642
44. Lebrun E., Fourel G., Defossez P.A., and Gilson E. A methyltransferase targeting assay reveals silencer-telomere interactions in budding yeast. Mol. Cell. Biol. 23 (2003) 1498-1508
45. Tomonaga T., Michelotti G.A., Libutti D., Uy A., Sauer B., and Levens D. Unrestraining genetic processes with a protein-DNA hinge. Mol. Cell 1 (1998) 759-764
46. He D.C., Martin T., and Penman S. Localization of heterogeneous nuclear ribonucleoprotein in the interphase nuclear matrix core filaments and on perichromosomal filaments at mitosis. Proc. Natl. Acad. Sci. USA 88 (1991) 7469-7473
47. Mattern K.A., Humbel B.M., Muijsers A.O., de Jong L., and van Driel R. hnRNP proteins and B23 are the major proteins of the internal nuclear matrix of HeLa S3 cells. J. Cell. Biochem. 62 (1996) 275-289
48. Samuel S.K., Spencer V.A., Bajno L., Sun J.M., Holth L.T., Oesterreich S., and Davie J.R. In situ cross-linking by cisplatin of nuclear matrix-bound transcription factors to nuclear DNA of human breast cancer cells. Cancer Res. 58 (1998) 3004-3008
49. Irie K., Tadauchi T., Takizawa P.A., Vale R.D., Matsumoto K., and Herskowitz I. The Khd1 protein, which has three KH RNA-binding motifs, is required for proper localization of ASH1 mRNA in yeast. EMBO J. 21 (2002) 1158-1167
50. Brachmann C.B., Davies A., Cost G.J., Caputo E., Li J., Hieter P., and Boeke J.D. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14 (1998) 115-132
51. Gietz R.D., and Woods R.A. Transformation of yeast by LiAc/SS carrier DNA/PEG method. Methods Enzymol. 350 (2002) 87-96
52. In: Adams A., Gottschling D.E., Kaiser C.A., and Stearns T. (Eds). Methods in Yeast Genetics (1997), Cold Spring Harbor Laboratory Press
53. Nelson J.D., Denisenko O., Sova P., and Bomsztyk K. Fast chromatin immunoprecipitation assay. Nucleic Acids Res. 34 (2006) e2