Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization

Cell

Volumn 117, Issue 4, 2004, Pages 427-439

  Casolari, Jason M ^a   Brown, Christopher R ^a   Komili, Suzanne ^a   West, Jason ^a   Hieronymus, Haley ^a   Silver, Pamela A ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GALACTOSE; GUANINE NUCLEOTIDE EXCHANGE FACTOR; KARYOPHERIN; NUCLEOPORIN; PROTEIN CSE1; PROTEIN MLP1; PROTEIN MLP2; PROTEIN NUP145; PROTEIN NUP2; PROTEIN NUP60; RAN PROTEIN; RAP PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL NUCLEUS; CONTROLLED STUDY; GENETIC TRANSCRIPTION; GENOME; NONHUMAN; NUCLEAR PORE; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION;

FUNGI; MYXOGASTRIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 2342501365     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(04)00448-9     Document Type: Article

References (63)

1. Aebi M., Clark M.W., Vijayraghavan U., Abelson J. A yeast mutant, PRP20, altered in mRNA metabolism and maintenance of the nuclear structure, is defective in a gene homologous to the human gene RCC1 which is involved in the control of chromosome condensation. Mol. Gen. Genet. 224:1990;72-80
2. Alter O., Brown P.O., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA. 97:2000;10101-10106
3. Amati B.B., Gasser S.M. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell. 54:1988;967-978
4. Amati B., Pick L., Laroche T., Gasser S.M. Nuclear scaffold attachment stimulates, but is not essential for ARS activity in Saccharomyces cerevisiae. analysis of the Drosophila ftz SAR EMBO J. 9:1990;4007-4016
5. Andrulis E.D., Neiman A.M., Zappulla D.C., Sternglanz R. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature. 394:1998;592-595
6. Andrulis E.D., Zappulla D.C., Ansari A., Perrod S., Laiosa C.V., Gartenberg M.R., Sternglanz R. Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Mol. Cell. Biol. 22:2002;8292-8301
7. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology. tool for the unification of biology The Gene Ontology Consortium. Nat. Genet. 25:2000;25-29
8. Azuma Y., Dasso M. The role of Ran in nuclear function. Curr. Opin. Cell Biol. 12:2000;302-307
9. Becskei A., Mattaj I.W. The strategy for coupling the RanGTP gradient to nuclear protein export. Proc. Natl. Acad. Sci. USA. 100:2003;1717-1722
10. Berriz G.F., King O.D., Bryant B., Sander C., Roth F.P. Characterizing gene sets with FuncAssociate. Bioinformatics. 19:2003;2502-2504
11. Blobel G. Gene gating. a hypothesis Proc. Natl. Acad. Sci. USA. 82:1985;8527-8529
12. Booth J.W., Belanger K.D., Sannella M.I., Davis L.I. The yeast nucleoporin Nup2p is involved in nuclear export of importin alpha/Srp1p. J. Biol. Chem. 274:1999;32360-32367
13. Brown K.E., Guest S.S., Smale S.T., Hahm K., Merkenschlager M., Fisher A.G. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell. 91:1997;845-854
14. Brown K.E., Baxter J., Graf D., Merkenschlager M., Fisher A.G. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell. 3:1999;207-217
15. Buchman A.R., Kimmerly W.J., Rine J., Kornberg R.D. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:1988;210-225
16. Clark K.L., Ohtsubo M., Nishimoto T., Goebl M., Sprague G.F. Jr. The yeast SRM1 protein and human RCC1 protein share analogous functions. Cell Regul. 2:1991;781-792
17. Damelin M., Simon I., Moy T.I., Wilson B., Komili S., Tempst P., Roth F.P., Young R.A., Cairns B.R., Silver P.A. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol. Cell. 9:2002;563-573
18. Dernburg A.F., Broman K.W., Fung J.C., Marshall W.F., Philips J., Agard D.A., Sedat J.W. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell. 85:1996;745-759
19. Emtage J.L., Bucci M., Watkins J.L., Wente S.R. Defining the essential functional regions of the nucleoporin Nup145p. J. Cell Sci. 110:1997;911-925
20. Fahrenkrog B., Hurt E.C., Aebi U., Pante N. Molecular architecture of the yeast nuclear pore complex. localization of Nsp1p subcomplexes J. Cell Biol. 143:1998;577-588
21. Feuerbach F., Galy V., Trelles-Sticken E., Fromont-Racine M., Jacquier A., Gilson E., Olivo-Marin J.C., Scherthan H., Nehrbass U. Nuclear architecture and spatial positioning help establish transcriptional states of telomeres in yeast. Nat. Cell Biol. 4:2002;214-221
22. Fontoura B.M., Blobel G., Yaseen N.R. The nucleoporin Nup98 is a site for GDP/GTP exchange on ran and termination of karyopherin beta 2-mediated nuclear import. J. Biol. Chem. 275:2000;31289-31296
23. Forrester W., Stutz F., Rosbash M., Wickens M. Defects in mRNA 3′-end formation, transcription initiation, and mRNA transport associated with the yeast mutation prp20. possible coupling of mRNA processing and chromatin structure Genes Dev. 6:1992;1914-1926
24. Freeman K.B., Karns L.R., Lutz K.A., Smith M.M. Histone H3 transcription in Saccharomyces cerevisiae is controlled by multiple cell cycle activation sites and a constitutive negative regulatory element. Mol. Cell. Biol. 12:1992;5455-5463
25. Galy V., Olivo-Marin J.C., Scherthan H., Doye V., Rascalou N., Nehrbass U. Nuclear pore complexes in the organization of silent telomeric chromatin. Nature. 403:2000;108-112
26. Galy V., Gadal O., Fromont-Racine M., Romano A., Jacquier A., Nehrbass U. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell. 116:2004;63-73
27. Gotta M., Gasser S.M. Nuclear organization and transcriptional silencing in yeast. Experientia. 52:1996;1136-1147
28. Gotta M., Laroche T., Gasser S.M. Analysis of nuclear organization in Saccharomyces cerevisiae. Methods Enzymol. 304:1999;663-672
29. Graham I.R., Chambers A. Use of a selection technique to identify the diversity of binding sites for the yeast RAP1 transcription factor. Nucleic Acids Res. 22:1994;124-130
30. Grandi P., Doye V., Hurt E.C. Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96. EMBO J. 12:1993;3061-3071
31. Green D.M., Johnson C.P., Hagan H., Corbett A.H. The C-terminal domain of myosin-like protein 1 (Mlp1p) is a docking site for heterogeneous nuclear ribonucleoproteins that are required for mRNA export. Proc. Natl. Acad. Sci. USA. 100:2003;1010-1015
32. Hediger F., Neumann F.R., Van Houwe G., Dubrana K., Gasser S.M. Live imaging of telomeres. yKu and Sir proteins define redundant telomere-anchoring pathways in yeast Curr. Biol. 12:2002;2076-2089
33. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95:1998;717-728
34. Hood J.K., Casolari J.M., Silver P.A. Nup2p is located on the nuclear side of the nuclear pore complex and coordinates Srp1p/importin-alpha export. J. Cell Sci. 113:2000;1471-1480
35. Huang L., Baldwin M.A., Maltby D.A., Medzihradszky K.F., Baker P.R., Allen N., Rexach M., Edmondson R.D., Campbell J., Juhasz P., et al. The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. Mol. Cell. Proteomics. 1:2002;434-450
36. Hughes J.D., Estep P.W., Tavazoie S., Church G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296:2000;1205-1214
37. Idrissi F.Z., Pina B. Functional divergence between the half-sites of the DNA-binding sequence for the yeast transcriptional regulator Rap1p. Biochem. J. 341:1999;477-482
38. Ishii K., Arib G., Lin C., Van Houwe G., Laemmli U.K. Chromatin boundaries in budding yeast. the nuclear pore connection Cell. 109:2002;551-562
39. Kadowaki T., Chen S., Hitomi M., Jacobs E., Kumagai C., Liang S., Schneiter R., Singleton D., Wisniewska J., Tartakoff A.M. Isolation and characterization of Saccharomyces cerevisiae mRNA transport-defective (mtr) mutants. J. Cell Biol. 126:1994;649-659
40. Klein F., Laroche T., Cardenas M.E., Hofmann J.F., Schweizer D., Gasser S.M. Localization of RAP1 and topoisomerase II in nuclei and meiotic chromosomes of yeast. J. Cell Biol. 117:1992;935-948
41. Knop M., Siegers K., Pereira G., Zachariae W., Winsor B., Nasmyth K., Schiebel E. Epitope tagging of yeast genes using a PCR-based strategy. more tags and improved practical routines Yeast. 15:1999;963-972
42. Kosova B., Pante N., Rollenhagen C., Podtelejnikov A., Mann M., Aebi U., Hurt E. Mlp2p, a component of nuclear pore attached intranuclear filaments, associates with nic96p. J. Biol. Chem. 275:2000;343-350
43. Krebber H., Taura T., Lee M.S., Silver P.A. Uncoupling of the hnRNP Npl3p from mRNAs during the stress-induced block in mRNA export. Genes Dev. 13:1999;1994-2004
44. Kuersten S., Ohno M., Mattaj I.W. Nucleocytoplasmic transport. Ran, beta and beyond Trends Cell Biol. 11:2001;497-503
45. Lascaris R.F., Mager W.H., Planta R.J. DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics. 15:1999;267-277
46. Lashkari D.A., DeRisi J.L., McCusker J.H., Namath A.F., Gentile C., Hwang S.Y., Brown P.O., Davis R.W. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA. 94:1997;13057-13062
47. Lieb J.D., Liu X., Botstein D., Brown P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:2001;327-334
48. Maillet L., Boscheron C., Gotta M., Marcand S., Gilson E., Gasser S.M. Evidence for silencing compartments within the yeast nucleus. a role for telomere proximity and Sir protein concentration in silencer-mediated repression Genes Dev. 10:1996;1796-1811
49. Marcand S., Buck S.W., Moretti P., Gilson E., Shore D. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap 1 protein. Genes Dev. 10:1996;1297-1309
50. Nemergut M.E., Mizzen C.A., Stukenberg T., Allis C.D., Macara I.G. Chromatin docking and exchange activity enhancement of RCC1 by histones H2A and H2B. Science. 292:2001;1540-1543
51. Ohtsubo M., Kai R., Furuno N., Sekiguchi T., Sekiguchi M., Hayashida H., Kuma K., Miyata T., Fukushige S., Murotsu T., et al. Isolation and characterization of the active cDNA of the human cell cycle gene (RCC1) involved in the regulation of onset of chromosome condensation. Genes Dev. 1:1987;585-593
52. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E., et al. Genome-wide location and function of DNA binding proteins. Science. 290:2000;2306-2309
53. Ren B., Cam H., Takahashi Y., Volkert T., Terragni J., Young R.A., Dynlacht B.D. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev. 16:2002;245-256
54. Shore D. Telomerase and telomere-binding proteins. controlling the endgame Trends Biochem. Sci. 22:1997;233-235
55. Stavenhagen J.B., Zakian V.A. Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae. Genes Dev. 8:1994;1411-1422
56. Strambio-de-Castillia C., Blobel G., Rout M.P. Proteins connecting the nuclear pore complex with the nuclear interior. J. Cell Biol. 144:1999;839-855
57. Suntharalingam M., Wente S.R. Peering through the pore. nuclear pore complex structure, assembly, and function Dev. Cell. 4:2003;775-789
58. Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., Church G.M. Systematic determination of genetic network architecture. Nat. Genet. 22:1999;281-285
59. Teixeira M.T., Siniossoglou S., Podtelejnikov S., Benichou J.C., Mann M., Dujon B., Hurt E., Fabre E. Two functionally distinct domains generated by in vivo cleavage of Nup145p. a novel biogenesis pathway for nucleoporins EMBO J. 16:1997;5086-5097
60. Teixeira M.T., Fabre E., Dujon B. Self-catalyzed cleavage of the yeast nucleoporin Nup145p precursor. J. Biol. Chem. 274:1999;32439-32444
61. Thompson J.S., Johnson L.M., Grunstein M. Specific repression of the yeast silent mating locus HMR by an adjacent telomere. Mol. Cell. Biol. 14:1994;446-455
62. Weis K. Regulating access to the genome. nucleocytoplasmic transport throughout the cell cycle Cell. 112:2003;441-451
63. Yu Q., Qiu R., Foland T.B., Griesen D., Galloway C.S., Chiu Y.H., Sandmeier J., Broach J.R., Bi X. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression. Nucleic Acids Res. 31:2003;1224-1233