Transcriptional regulation at the yeast nuclear envelope

Nucleus (United States)

Volumn 4, Issue 5, 2013, Pages

  Steglich, Babett ^a   Sazer, Shelley ^b   Ekwall, Karl ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Heterochromatin; Nuclear envelope; Nuclear pore complex; Telomeres; Transcriptional regulation

Indexed keywords

HISTONE ACETYLTRANSFERASE GCN5; NUCLEOPORIN; RAP1 PROTEIN; TELOMERASE; TRANSCRIPTION FACTOR GAL4; TRANSCRIPTION FACTOR IIIB;

CELL NUCLEUS MEMBRANE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA REPAIR; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE SILENCING; GENETIC RECOMBINATION; GENOMIC INSTABILITY; HISTONE METHYLATION; NONHUMAN; NUCLEAR PORE; REPORTER GENE; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; ANIMAL; CYTOLOGY; FUNGAL GENOME; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HETEROCHROMATIN; HUMAN; NUCLEAR PORE COMPLEX; TELOMERE; TELOMERES; TRANSCRIPTIONAL REGULATION; YEAST;

METAZOA;

HETEROCHROMATIN; NUCLEAR ENVELOPE; NUCLEAR PORE COMPLEX; TELOMERES; TRANSCRIPTIONAL REGULATION;

ANIMALS; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; HUMANS; NUCLEAR ENVELOPE; TELOMERE; TRANSCRIPTION, GENETIC; YEASTS;

EID: 84887476450     PISSN: 19491034     EISSN: 19491042     Source Type: Journal    
DOI: 10.4161/nucl.26394     Document Type: Review

References (112)

1. Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol 2010; 2:a003889. PMID:20300217; http://dx.doi.org/10.1101/cshperspect. a003889.
2. Molnar M, Kleckner N. Examination of interchromosomal interactions in vegetatively growing diploid Schizosaccharomyces pombe cells by Cre/loxP sitespecific recombination. Genetics 2008; 178:99-112. PMID:18202361; http://dx.doi.org/10.1534/genetics. 107.082826.
3. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature 2010; 465:363-7. PMID:20436457; http://dx.doi.org/10.1038/nature08973.
4. Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, Noma K-II. Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res 2010; 38:8164-77. PMID:21030438; http://dx.doi.org/10.1093/nar/gkq955.
5. Boyle S, Gilchrist S, Bridger JM, Mahy NL, Ellis JA, Bickmore WA. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 2001; 10:211-9. PMID:11159939; http://dx.doi.org/10.1093/hmg/10.3.211.
6. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948-51. PMID:18463634; http://dx.doi.org/10.1038/nature06947.
7. Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell 2009; 137:1194-211. PMID:19563753; http://dx.doi.org/10.1016/j.cell.2009.06.001.
8. Sutherland H, Bickmore WA. Transcription factories: gene expression in unions? Nat Rev Genet 2009; 10:457-66. PMID:19506577; http://dx.doi.org/10.1038/nrg2592.
9. Chagin VO, Stear JH, Cardoso MC.organization of DNA replication. Cold Spring Harb Perspect Biol 2010; 2:a000737-000737. PMID:20452942; http://dx.doi.org/10.1101/cshperspect.a000737.
10. Giglia-Mari G, Zotter A, Vermeulen W. DNA damage response. Cold Spring Harb Perspect Biol 2011; 3:a000745. PMID:20980439; http://dx.doi.org/10.1101/cshperspect.a000745.
11. Wansink DG, Schul W, van der Kraan I, van Steensel B, van Driel R, de Jong L. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J Cell Biol 1993; 122:283-93. PMID:8320255; http://dx.doi.org/10.1083/jcb.122.2.283.
12. Brand AH, Perrimon N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 1993; 118:401-15. PMID:8223268.
13. Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 1998; 394:592-5. PMID:9707122; http://dx.doi.org/10.1038/29100.
14. 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 2002; 4:214-21. PMID:11862215; http://dx.doi.org/10.1038/ncb756.
15. Strambio-de-Castillia C, Blobel G, Rout MP. Proteins connecting the nuclear pore complex with the nuclear interior. J Cell Biol 1999; 144:839-55. PMID:10085285; http://dx.doi.org/10.1083/jcb.144.5.839.
16. Krull S, Dörries J, Boysen B, Reidenbach S, Magnius L, Norder H, Thyberg J, Cordes VC. Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion. EMBO J 2010; 29:1659-73. PMID:20407419; http://dx.doi.org/10.1038/emboj.2010.54.
17. Kumaran RI, Spector DL. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 2008; 180:51-65. PMID:18195101; http://dx.doi.org/10.1083/jcb.200706060.
18. Reddy KL, Zullo JM, Bertolino E, Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 2008; 452:243-7. PMID:18272965; http://dx.doi.org/10.1038/nature06727.
19. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 2008; 4:e1000039. PMID:18369458; http://dx.doi.org/10.1371/journal.pgen.1000039.
20. Dialynas G, Speese S, Budnik V, Geyer PK, Wallrath LL. The role of Drosophila Lamin C in muscle function and gene expression. Development 2010; 137:3067-77. PMID:20702563; http://dx.doi.org/10.1242/dev.048231.
21. Ruault M, Dubarry M, Taddei A. Re-positioning genes to the nuclear envelope in mammalian cells: impact on transcription. Trends Genet 2008; 24:574-81. PMID:18819723; http://dx.doi.org/10.1016/j. tig.2008.08.008.
22. Towbin BD, Meister P, Gasser SM. The nuclear envelope--a scaffold for silencing? Curr Opin Genet Dev 2009; 19:180-6. PMID:19303765; http://dx.doi.org/10.1016/j.gde.2009.01.006.
23. Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 2006; 38:1005-14. PMID:16878134; http://dx.doi.org/10.1038/ng1852.
24. Steglich B, Filion GJ, van Steensel B, Ekwall K. The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe. Nucleus 2012; 3:77-87. PMID:22156748; http://dx.doi.org/10.4161/nucl.18825.
25. Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004; 117:427-39. PMID:15137937; http://dx.doi.org/10.1016/S0092-8674(04)00448-9.
26. Brickner JH, Walter P. Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2004; 2:e342. PMID:15455074; http://dx.doi.org/10.1371/journal.pbio.0020342.
27. Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, Buc H, Feuerbach-Fournier F, Olivo-Marin J-C, Hurt EC, et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 2006; 441:770-3. PMID:16760982; http://dx.doi.org/10.1038/nature04752.
28. Larschan E, Winston F. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 2001; 15:1946-56. PMID:11485989; http://dx.doi.org/10.1101/gad.911501.
29. Bhaumik SR, Green MR. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes Dev 2001; 15:1935-45. PMID:11485988; http://dx.doi.org/10.1101/gad.911401.
30. Huisinga KL, Pugh BF. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell 2004; 13:573-85. PMID:14992726; http://dx.doi.org/10.1016/S1097-2765(04)00087-5.
31. Rodríguez-Navarro S, Fischer T, Luo M-J, Antúnez O, Brettschneider S, Lechner J, Pérez-Ortín JE, Reed R, Hurt E. Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell 2004; 116:75-86. PMID:14718168; http://dx.doi.org/10.1016/S0092-8674(03)01025-0.
32. Fischer T, Strässer K, Rácz A, Rodriguez-Navarro S, Oppizzi M, Ihrig P, Lechner J, Hurt E. The mRNA export machinery requires the novel Sac3p-Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. EMBO J 2002; 21:5843-52. PMID:12411502; http://dx.doi.org/10.1093/emboj/cdf590.
33. Brickner DG, Cajigas I, Fondufe-Mittendorf Y, Ahmed S, Lee P-C, Widom J, Brickner JH. H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 2007; 5:e81. PMID:17373856; http://dx.doi.org/10.1371/journal.pbio.0050081.
34. Ahmed S, Brickner DG, Light WH, Cajigas I, McDonough M, Froyshteter AB, Volpe T, Brickner JH. DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery. Nat Cell Biol 2010; 12:111-8. PMID:20098417; http://dx.doi.org/10.1038/ncb2011.
35. Brickner DG, Ahmed S, Meldi L, Thompson A, Light W, Young M, Hickman TL, Chu F, Fabre E, Brickner JH. Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev Cell 2012; 22:1234-46. PMID:22579222; http://dx.doi.org/10.1016/j.devcel. 2012.03.012.
36. Kundu S, Horn PJ, Peterson CL. SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev 2007; 21:997-1004. PMID:17438002; http://dx.doi.org/10.1101/gad.1506607
37. Zacharioudakis I, Gligoris T, Tzamarias D. A yeast catabolic enzyme controls transcriptional memory. Curr Biol 2007; 17:2041-6. PMID:17997309; http://dx.doi.org/10.1016/j.cub.2007.10.044.
38. Adam M, Robert F, Larochelle M, Gaudreau L. H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol Cell Biol 2001; 21:6270-9. PMID:11509669; http://dx.doi.org/10.1128/MCB.21.18.6270-6279.2001.
39. Hardy S, Jacques P-E, Gévry N, Forest A, Fortin M-E, Laflamme L, Gaudreau L, Robert F. The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition. PLoS Genet 2009; 5:e1000687. PMID:19834540; http://dx.doi.org/10.1371/journal.pgen.1000687.
40. Kundu S, Peterson CL. Dominant role for signal transduction in the transcriptional memory of yeast GAL genes. Mol Cell Biol 2010; 30:2330-40. PMID:20212085; http://dx.doi.org/10.1128/MCB.01675-09.
41. Tan-Wong SM, Wijayatilake HD, Proudfoot NJ. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev 2009; 23:2610-24. PMID:19933151; http://dx.doi.org/10.1101/gad.1823209.
42. Light WH, Brickner DG, Brand VR, Brickner JH. Interaction of a DNA zip code with the nuclear pore complex promotes H2A.Z incorporation and INO1 transcriptional memory. Mol Cell 2010; 40:112-25. PMID:20932479; http://dx.doi.org/10.1016/j.molcel. 2010.09.007.
43. Yoshida T, Shimada K, Oma Y, Kalck V, Akimura K, Taddei A, Iwahashi H, Kugou K, Ohta K, Gasser SM, et al. Actin-related protein Arp6 influences H2A.Zdependent and-independent gene expression and links ribosomal protein genes to nuclear pores. PLoS Genet 2010; 6:e1000910. PMID:20419146; http://dx.doi.org/10.1371/journal.pgen.1000910.
44. Gard S, Light W, Xiong B, Bose T, McNairn AJ, Harris B, Fleharty B, Seidel C, Brickner JH, Gerton JL. Cohesinopathy mutations disrupt the subnuclear organization of chromatin. J Cell Biol 2009; 187:455-62. PMID:19948494; http://dx.doi.org/10.1083/jcb.200906075.
45. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 2002; 297:1833-7. PMID:12193640; http://dx.doi.org/10.1126/science.1074973.
46. Gullerova M, Moazed D, Proudfoot NJ. Autoregulation of convergent RNAi genes in fission yeast. Genes Dev 2011; 25:556-68. PMID:21357674; http://dx.doi.org/10.1101/gad.618611.
47. Zhang K, Fischer T, Porter RL, Dhakshnamoorthy J, Zofall M, Zhou M, Veenstra T, Grewal SIS. Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA. Science 2011; 331:1624-7. PMID:21436456; http://dx.doi.org/10.1126/science.1198712.
48. Woolcock KJ, Stunnenberg R, Gaidatzis D, Hotz H-R, Emmerth S, Barraud P, Bühler M. RNAi keeps Atf1-bound stress response genes in check at nuclear pores. Genes Dev 2012; 26:683-92. PMID:22431512; http://dx.doi.org/10.1101/gad.186866.112.
49. Haber JE. Mating-type genes and MAT switching in Saccharomyces cerevisiae. Genetics 2012; 191:33-64. PMID:22555442; http://dx.doi.org/10.1534/genetics.111.134577.
50. Klar AJS. Lessons learned from studies of fission yeast mating-type switching and silencing. Annu Rev Genet 2007; 41:213-36. PMID:17614787; http://dx.doi.org/10.1146/annurev.genet.39.073103.094316.
51. Tanny JC, Dowd GJ, Huang J, Hilz H, Moazed D. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 1999; 99:735-45. PMID:10619427; http://dx.doi.org/10.1016/S0092-8674(00)81671-2.
52. Imai S, Armstrong CM, Kaeberlein M, Guarente L. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 2000; 403:795-800. PMID:10693811; http://dx.doi.org/10.1038/35001622.
53. Suka N, Luo K, Grunstein M. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat Genet 2002; 32:378-83. PMID:12379856; http://dx.doi.org/10.1038/ng1017.
54. Fox CA, McConnell KH. Toward biochemical understanding of a transcriptionally silenced chromosomal domain in Saccharomyces cerevisiae. J Biol Chem 2005; 280:8629-32. PMID:15623501; http://dx.doi.org/10.1074/jbc.R400033200.
55. Thompson-Stewart D, Karpen GH, Spradling AC. A transposable element can drive the concerted evolution of tandemly repetitious DNA. Proc Natl Acad Sci U S A 1994; 91:9042-6. PMID:8090766; http://dx.doi.org/10.1073/pnas.91.19.9042.
56. Shei GJ, Broach JR. Yeast silencers can act as orientation-dependent gene inactivation centers that respond to environmental signals. Mol Cell Biol 1995; 15:3496-506. PMID:7791756.
57. Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM. Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev 1996; 10:1796-811. PMID:8698239; http://dx.doi.org/10.1101/gad.10.14.1796.
58. Marcand S, Buck SW, 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 1996; 10:1297-309. PMID:8647429; http://dx.doi.org/10.1101/gad.10.11.1297.
59. Bystricky K, Van Attikum H, Montiel M-D, Dion V, Gehlen L, Gasser SM. Regulation of nuclear positioning and dynamics of the silent mating type loci by the yeast Ku70/Ku80 complex. Mol Cell Biol 2009; 29:835-48. PMID:19047366; http://dx.doi.org/10.1128/MCB.01009-08.
60. Miele A, Bystricky K, Dekker J. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet 2009; 5:e1000478. PMID:19424429; http://dx.doi.org/10.1371/journal.pgen.1000478.
61. Ruben GJ, Kirkland JG, MacDonough T, Chen M, Dubey RN, Gartenberg MR, Kamakaka RT. Nucleoporin mediated nuclear positioning and silencing of HMR. PLoS One 2011; 6:e21923. PMID:21818277; http://dx.doi.org/10.1371/journal. pone.0021923.
62. Gartenberg MR, Neumann FR, Laroche T, Blaszczyk M, Gasser SM. Sir-mediated repression can occur independently of chromosomal and subnuclear contexts. Cell 2004; 119:955-67. PMID:15620354; http://dx.doi.org/10.1016/j.cell.2004.11.008.
63. Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 2002; 109:551-62. PMID:12062099; http://dx.doi.org/10.1016/S0092-8674(02)00756-0.
64. Grewal SIS, Klar AJ. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast. Genetics 1997; 146:1221-38. PMID:9258669.
65. Thon G, Friis T. Epigenetic inheritance of transcriptional silencing and switching competence in fission yeast. Genetics 1997; 145:685-96. PMID:9055078.
66. Hall IM, Shankaranarayana GD, Noma K-II, Ayoub N, Cohen A, Grewal SIS. Establishment and maintenance of a heterochromatin domain. Science 2002; 297:2232-7. PMID:12215653; http://dx.doi.org/10.1126/science.1076466.
67. Martienssen RA, Zaratiegui M, Goto DB. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. Trends Genet 2005; 21:450-6. PMID:15979194; http://dx.doi.org/10.1016/j.tig.2005.06.005.
68. Ekwall K, Javerzat JP, Lorentz A, Schmidt H, Cranston G, Allshire RC. The chromodomain protein Swi6: a key component at fission yeast centromeres. Science 1995; 269:1429-31. PMID:7660126; http://dx.doi.org/10.1126/science.7660126.
69. Noma K, Allis CD, Grewal SIS. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science 2001; 293:1150-5. PMID:11498594; http://dx.doi.org/10.1126/science. 1064150.
70. Alfredsson-Timmins J, Henningson F, Bjerling P. The Clr4 methyltransferase determines the subnuclear localization of the mating-type region in fission yeast. J Cell Sci 2007; 120:1935-43. PMID:17504808; http://dx.doi.org/10.1242/jcs.03457.
71. Luo K, Vega-Palas MA, Grunstein M. Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev 2002; 16:1528-39. PMID:12080091; http://dx.doi.org/10.1101/gad.988802.
72. Gravel S, Larrivée M, Labrecque P, Wellinger RJ. Yeast Ku as a regulator of chromosomal DNA end structure. Science 1998; 280:741-4. PMID:9563951; http://dx.doi.org/10.1126/science.280.5364.741.
73. Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 1999; 97:621-33. PMID:10367891; http://dx.doi.org/10.1016/S0092-8674(00)80773-4.
74. Huang Y. Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res 2002; 30:1465-82. PMID:11917007; http://dx.doi.org/10.1093/nar/30.7.1465.
75. Taddei A, Hediger F, Neumann FR, Bauer C, Gasser SM. Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. EMBO J 2004; 23:1301-12. PMID:15014445; http://dx.doi.org/10.1038/sj.emboj.7600144.
76. Bupp JM, Martin AE, Stensrud ES, Jaspersen SL. Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3. J Cell Biol 2007; 179:845-54. PMID:18039933; http://dx.doi.org/10.1083/jcb.200706040.
77. Schober H, Ferreira H, Kalck V, Gehlen LR, Gasser SM. Yeast telomerase and the SUN domain protein Mps3 anchor telomeres and repress subtelomeric recombination. Genes Dev 2009; 23:928-38. PMID:19390087; http://dx.doi.org/10.1101/gad.1787509.
78. Bühler M, Gasser SM. Silent chromatin at the middle and ends: lessons from yeasts. EMBO J 2009; 28:2149-61. PMID:19629038; http://dx.doi.org/10.1038/emboj.2009.185.
79. Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM. The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion. Genome Res 2009; 19:611-25. PMID:19179643; http://dx.doi.org/10.1101/gr.083881.108.
80. Galy V, Olivo-Marin JC, Scherthan H, Doye V, Rascalou N, Nehrbass U. Nuclear pore complexes in the organization of silent telomeric chromatin. Nature 2000; 403:108-12. PMID:10638763; http://dx.doi.org/10.1038/47528.
81. Van de Vosse DW, Wan Y, Lapetina DL, Chen W-M, Chiang J-H, Aitchison JD, Wozniak RW. A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 2013; 152:969-83. PMID:23452847; http://dx.doi.org/10.1016/j.cell.2013.01.049.
82. Funabiki H, Hagan IM, Uzawa S, Yanagida M. Cell cycle-dependent specific positioning and clustering of centromeres and telomeres in fission yeast. J Cell Biol 1993; 121:961-76. PMID:8388878; http://dx.doi.org/10.1083/jcb.121.5.961.
83. Chikashige Y, Tsutsumi C, Yamane M, Okamasa K, Haraguchi T, Hiraoka Y. Meiotic proteins bqt1 and bqt2 tether telomeres to form the bouquet arrangement of chromosomes. Cell 2006; 125:59-69. PMID:16615890; http://dx.doi.org/10.1016/j. cell.2006.01.048.
84. Chikashige Y, Yamane M, Okamasa K, Tsutsumi C, Kojidani T, Sato M, Haraguchi T, Hiraoka Y. Membrane proteins Bqt3 and-4 anchor telomeres to the nuclear envelope to ensure chromosomal bouquet formation. J Cell Biol 2009; 187:413-27. PMID:19948484; http://dx.doi.org/10.1083/jcb.200902122.
85. Fujita I, Nishihara Y, Tanaka M, Tsujii H, Chikashige Y, Watanabe Y, Saito M, Ishikawa F, Hiraoka Y, Kanoh J. Telomere-nuclear envelope dissociation promoted by Rap1 phosphorylation ensures faithful chromosome segregation. Curr Biol 2012; 22:1932-7. PMID:22959349; http://dx.doi.org/10.1016/j. cub.2012.08.019.
86. Gonzalez Y, Saito A, Sazer S. Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina. Nucleus 2012; 3:60-76. PMID:22540024; http://dx.doi.org/10.4161/nucl.18824.
87. Brachner A, Foisner R. Evolvement of LEM proteins as chromatin tethers at the nuclear periphery. Biochem Soc Trans 2011; 39:1735-41. PMID:22103517; http://dx.doi.org/10.1042/BST20110724.
88. Tanaka A, Tanizawa H, Sriswasdi S, Iwasaki O, Chatterjee AG, Speicher DW, Levin HL, Noguchi E, Noma K-II. Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation. Mol Cell 2012; 48:532-46. PMID:23084836; http://dx.doi.org/10.1016/j.molcel.2012.09.011.
89. Buchanan L, Durand-Dubief M, Roguev A, Sakalar C, Wilhelm B, Strålfors A, Shevchenko A, Aasland R, Shevchenko A, Ekwall K, et al. The Schizosaccharomyces pombe JmjC-protein, Msc1, prevents H2A.Z localization in centromeric and subtelomeric chromatin domains. PLoS Genet 2009; 5:e1000726. PMID:19911051; http://dx.doi.org/10.1371/journal.pgen.1000726.
90. Strålfors A, Walfridsson J, Bhuiyan H, Ekwall K. The FUN30 chromatin remodeler, Fft3, protects centromeric and subtelomeric domains from euchromatin formation. PLoS Genet 2011; 7:e1001334. PMID:21437270; http://dx.doi.org/10.1371/journal. pgen.1001334.
91. Cam HP, Sugiyama T, Chen ES, Chen X, FitzGerald PC, Grewal SIS. Comprehensive analysis of heterochromatin-and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 2005; 37:809-19. PMID:15976807; http://dx.doi.org/10.1038/ng1602.
92. Sugiyama T, Cam HP, Sugiyama R, Noma K-II, Zofall M, Kobayashi R, Grewal SIS. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 2007; 128:491-504. PMID:17289569; http://dx.doi.org/10.1016/j.cell.2006.12.035.
93. Tomita K, Cooper JP. Fission yeast Ccq1 is telomerase recruiter and local checkpoint controller. Genes Dev 2008; 22:3461-74. PMID:19141478; http://dx.doi.org/10.1101/gad.498608.
94. Alfredsson-Timmins J, Kristell C, Henningson F, Lyckman S, Bjerling P. Reorganization of chromatin is an early response to nitrogen starvation in Schizosaccharomyces pombe. Chromosoma 2009; 118:99-112. PMID:18936951; http://dx.doi.org/10.1007/s00412-008-0180-6.
95. Dheur S, Saupe SJ, Genier S, Vazquez S, Javerzat J-P. Role for cohesin in the formation of a heterochromatic domain at fission yeast subtelomeres. Mol Cell Biol 2011; 31:1088-97. PMID:21189291; http://dx.doi.org/10.1128/MCB.01290-10.
96. Sinclair DA, Guarente L. Extrachromosomal rDNA circles--a cause of aging in yeast. Cell 1997; 91:1033-42. PMID:9428525; http://dx.doi.org/10.1016/S0092-8674(00)80493-6.
97. Mekhail K, Seebacher J, Gygi SP, Moazed D. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 2008; 456:667-70. PMID:18997772; http://dx.doi.org/10.1038/nature07460.
98. Chan JNY, Poon BPK, Salvi J, Olsen JB, Emili A, Mekhail K. Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains. Dev Cell 2011; 20:867-79. PMID:21664583; http://dx.doi.org/10.1016/j.devcel.2011.05.014.
99. Poon BPK, Mekhail K. Cohesin and related coiled-coil domain-containing complexes physically and functionally connect the dots across the genome. Cell Cycle 2011; 10:2669-82. PMID:21822055; http://dx.doi.org/10.4161/cc.10.16.17113.
100. Therizols P, Fairhead C, Cabal GG, Genovesio A, Olivo-Marin J-C, Dujon B, Fabre E. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J Cell Biol 2006; 172:189-99. PMID:16418532; http://dx.doi.org/10.1083/jcb.200505159.
101. Palancade B, Liu X, Garcia-Rubio M, Aguilera A, Zhao X, Doye V. Nucleoporins prevent DNA damage accumulation by modulating Ulp1-dependent sumoylation processes. Mol Biol Cell 2007; 18:2912-23. PMID:17538013; http://dx.doi.org/10.1091/mbc. E07-02-0123.
102. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ. Functional targeting of DNA damage to a nuclear pore-associated SUMOdependent ubiquitin ligase. Science 2008; 322:597-602. PMID:18948542; http://dx.doi.org/10.1126/science.1162790.
103. Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev 2009; 23:912-27. PMID:19390086; http://dx.doi.org/10.1101/gad.1782209.
104. Pinheiro I, Margueron R, Shukeir N, Eisold M, Fritzsch C, Richter FM, Mittler G, Genoud C, Goyama S, Kurokawa M, et al. Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity. Cell 2012; 150:948-60. PMID:22939622; http://dx.doi.org/10.1016/j. cell.2012.06.048.
105. Towbin BD, González-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM. Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 2012; 150:934-47. PMID:22939621; http://dx.doi.org/10.1016/j. cell.2012.06.051.
106. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 2010; 38:603-13. PMID:20513434; http://dx.doi.org/10.1016/j.molcel.2010.03.016.
107. Ikegami K, Egelhofer TA, Strome S, Lieb JD. Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol 2010; 11:R120. PMID:21176223; http://dx.doi.org/10.1186/gb-2010-11-12-r120.
108. Kalverda B, Pickersgill H, Shloma VV, Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010; 140:360-71. PMID:20144760; http://dx.doi.org/10.1016/j.cell.2010.01.011.
109. Neumann FR, Dion V, Gehlen LR, Tsai-Pflugfelder M, Schmid R, Taddei A, Gasser SM. Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination. Genes Dev 2012; 26:369-83. PMID:22345518; http://dx.doi.org/10.1101/gad.176156.111.
110. Oma Y, Harata M. Actin-related proteins localized in the nucleus: from discovery to novel roles in nuclear organization. Nucleus 2011; 2:38-46. PMID:21647298; http://dx.doi.org/10.4161/nucl.2.1.14510.
111. Dundr M, Ospina JK, Sung MH, John S, Upender M, Ried T, Hager GL, Matera AG. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol 2007; 179:1095-103. PMID:18070915; http://dx.doi.org/10.1083/jcb.200710058.
112. Sarshad A, Sadeghifar F, Louvet E, Mori R, Böhm S, Al-Muzzaini B, Vintermist A, Fomproix N, Östlund A-K, Percipalle P. Nuclear myosin 1c facilitates the chromatin modifications required to activate rRNA gene transcription and cell cycle progression. PLoS Genet 2013; 9:e1003397. PMID:23555303; http://dx.doi.org/10.1371/journal.pgen.1003397