Silencing in yeast rDNA chromatin: Reciprocal relationship in gene expression between RNA polymerase I and II

Molecular Cell

Volumn 12, Issue 1, 2003, Pages 135-145

  Cioci, Francesco ^a   Vu, Loan ^a   Eliason, Kristilyn ^a   Oakes, Melanie ^a   Siddiqi, Imran N ^a,b   Nomura, Masayasu ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; FUNGAL DNA; MUTANT PROTEIN; RIBOSOME DNA; RNA POLYMERASE II;

ARTICLE; CHROMATIN; FUNGAL GENETICS; GENE EXPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; NONHUMAN; PROMOTER REGION; REPORTER GENE; YEAST;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0043172404     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(03)00262-4     Document Type: Article

References (41)

1. Brill S.J., Sternglanz R. Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants. Cell. 54:1988;403-411.
2. Bryk M., Banerjee M., Murphy M., Knudsen K.E., Garfinkel D.J., Curcio M.J. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11:1997;255-269.
3. Bryk M., Briggs S.D., Strahl B.D., Curcio M.J., Allis C.D., Winston F. Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisiae by a Sir2-independent mechanism. Curr. Biol. 12:2002;165-170.
4. Buck S.W., Sandmeier J.J., Smith J.S. RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin. Cell. 111:2002;1003-1014.
5. Chernoff Y.O., Vincent A., Liebman S.W. Mutations in eukaryotic 18S ribosomal RNA affect translational fidelity and resistance to aminoglycoside antibiotics. EMBO J. 13:1994;906-913.
6. Dammann R., Lucchini R., Koller T., Sogo J.M. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21:1993;2331-2338.
7. Dammann R., Lucchini R., Koller T., Sogo J.M. Transcription in the yeast rRNA gene locus. distribution of the active gene copies and chromatin structure of their flanking regulatory sequences Mol. Cell. Biol. 15:1995;5294-5303.
8. French S.L., Osheim Y.N., Cioci F., Nomura M., Beyer A.L. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than the number of active genes. Mol. Cell. Biol. 23:2003;1558-1568.
9. Fritze C.E., Verschueren K., Strich R., Esposito R.E. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16:1997;6495-6509.
10. Gasser S.M., Cockell M.M. The molecular biology of the SIR proteins. Gene. 279:2001;1-16.
11. Gottlieb S., Esposito R.E. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell. 56:1989;771-776.
12. Grewal S.I.S., Elgin S.C.R. Heterochromatin. New possibilities for the inheritance of structure Curr. Opin. Genet. Dev. 12:2002;178-187.
13. Jenuwein J., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
14. Keener J., Dodd J.A., Lalo D., Nomura M. Histones H3 and H4 are components of upstream activation factor required for the high-level transcription of yeast rDNA by RNA polymerase I. Proc. Natl. Acad. Sci. USA. 94:1997;13458-13462.
15. Keys D.A., Lee B.-S., Dodd J.A., Nguyen T.T., Vu L., Fantino E., Burson L.M., Nogi Y., Nomura M. Multiprotein transcription factor UAF interacts with the upstream element of yeast RNA polymerase I promoter and forms a stable preinitiation complex. Genes Dev. 10:1996;887-903.
16. Kobayashi T., Heck D.J., Nomura M., Horiuchi T. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae. requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I Genes Dev. 12:1998;3821-3830.
17. Kobayashi T., Nomura M., Horiuchi T. Identification of DNA cis-elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 21:2001;136-147.
18. Lang W.H., Morrow B.E., Ju Q., Warner J.R., Reeder R.H. A model for transcription termination by RNA polymerase I. Cell. 79:1994;527-534.
19. Loidl P., Lucchini R., Sogo J.M. Histone composition and core histone acetylation of transcriptionally active ribosomal chromatin of physarum polycephalum. Cell Biol. Int. Rep. 16:1992;1177-1183.
20. Moazed D. Common theses in mechanisms of gene silencing. Mol. Cell. 8:2001;489-498.
21. Mutskov V.J., Russanova V.R., Dimitrov S.I., Pashev I.G. Histones associated with non-nucleosomal rat ribosomal genes are acetylated while those bound to nucleosome-organized gene copies are not. J. Biol. Chem. 271:1996;11852-11857.
22. Nogi Y., Yano R., Nomura M. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc. Natl. Acad. Sci. USA. 88:1991;3962-3966.
23. Nogi Y., Yano R., Dodd J., Carles C., Nomura M. Gene RRN4 in Saccharomyces cerevisiae encodes the A12.2 subunit of RNA polymerase I and is essential only at high temperatures. Mol. Cell. Biol. 13:1993;114-122.
24. Oakes M., Aris J.P., Brockenbrough J.S., Wai H., Vu L., Nomura M. Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae. J. Cell Biol. 143:1998;23-34.
25. Oakes M., Siddiqi I., Vu L., Aris J., Nomura M. Transcription factor UAF, expansion/contraction of rDNA repeats and RNA polymerase switch in the transcription of yeast rDNA. Mol. Cell. Biol. 19:1999;8559-8569.
26. Sherman, F., Fink, G.R., and Hicks, J.B. (1986). Laboratory Course Manual for Methods in Yeast Genetics. (Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y.).
27. Shou W., Sakamoto K.M., Keener J., Morimoto K.W., Traverso E.E., Azzam R., Hoppe G.J., Feldman R.M.R., DeModena J., Moazed D.et al. Net1 stimulates RNA Polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit. Mol. Cell. 8:2001;45-55.
28. Siddiqi I.N., Dodd J.A., Vu L., Eliason K., Oakes M.L., Keener J., Moore R., Young M.K., Nomura M. Transcription of chromosomal rRNA genes by both RNA polymerase I and II in yeast uaf30 mutants lacking the 30 kDa subunit of transcription factor UAF. EMBO J. 20:2001;4512-4521.
29. Sikorski R.S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 122:1989;19-27.
30. Smith J.S., Boeke J.D. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:1997;241-254.
31. Smith J.S., Brachmann C.B., Pillus L., Boeke J.D. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. Genetics. 149:1998;1205-1219.
32. Smith J.S., Caputo E., 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.
33. Straight A.F., Shou W., Dowd G.J., Turck C.W., Deshaies R.J., Johnson A.D., Moazed D. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell. 97:1999;245-256.
34. Sun Z.-W., Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 152:1999;921-932.
35. Voelkel-Meiman K., Keil R.L., Roeder G.S. Recombination-stimulating sequences in yeast ribosomal DNA correspond to sequences regulating transcription by RNA polymerase I. Cell. 48:1987;1071-1079.
36. Vu L., Siddiqi I., Lee B.-S., Josaitis C.A., Nomura M. RNA polymerase switch in transcription of yeast rDNA. Role of transcription factor UAF (upstream activation factor) in silencing rDNA transcription by RNA polymerase II Proc. Natl. Acad. Sci. USA. 96:1999;4390-4395.
37. Wai H., Vu L., Oakes M., Nomura M. Complete deletion of yeast chromosomal rDNA repeats and integration of a new rDNA repeat. use of rDNA deletion strains for functional analysis of rDNA promoter elements in vivo Nucleic Acids Res. 28:2000;3524-3534.
38. Wai H., Johzuka K., Vu L., Eliason K., Kobayashi T., Horiuchi T., Nomura M. Yeast RNA polymerase I enhancer is dispensable for transcription of chromosomal rDNA and cell growth and its apparent transcription enhancement from ectopic promoters requires Fob1 protein. Mol. Cell. Biol. 21:2001;5541-5553.
39. Wakimoto B.T. Beyond the nucleosome. epigenetic aspects of position-effect variegation in Drosophila Cell. 93:1998;321-324.
40. Weiler K.S., Wakimoto B.T. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29:1995;577-605.
41. Wittekind M., Dodd J., Vu L., Kolb J.M., Buhler J.-M., Sentenac A., Nomura M. Isolation and characterization of temperature-sensitive mutations in RPA190, the gene encoding the largest subunit of RNA polymerase I from Saccharomyces cerevisiae. Mol. Cell. Biol. 8:1988;3997-4008.