Supplementary Figures
Supplementary Figure 1: The sensitivity of the HA-Yra1(1-210) mutant to the anti-microtubule drug benomyl is enhanced in Δbub2 and Δmad3.
Spot test analysis of HA-Yra1 mutants in the presence of DMSO 2% (no drug control), benomyl 15µg/ml, benomyl 18µg/ml, benomyl 20µg/ml, benomyl 23µg/ml, at 30°C and 34°C. Confluent cultures of HA-Yra1 mutants shuffled into WT or Δbub2, Δmad3, and Δkar9 strains were serially diluted and spotted on the indicated plates. Sensitivity and sickness is shown by *; additive effects by **. The corresponding spot tests at 25°C are shown in Figure 5.2.
Supplementary Figure 2: Yra1 half-life IR is lengthened by 30 min and correlates with decreased Yra1 ubiquitination.
A) Protein stability assay using metabolic depletion of GAL-HA-YRA1 in presence of the endogenous wild-type YRA1 gene post irradiation (IR= 50γ) or without treatment (WT).
YRA1 WT shuffle cells expressing HA-Yra1 from the GAL promoter on a centromeric plasmid were grown over-night in selective medium containing 2% galactose. Cells at OD=0.3 were irradiated (IR=
50γ) or not (WT) and shifted to selective medium containing 2% glucose to repress GAL-HA-YRA1 and collected at time 0, 1h, 2h, 3h, 4h, 5h, 6h, and 7h following glucose addition. WB analysis and Yra1 protein quantification were performed as described in Figure 1.1. The average of 3 independent experiments (N3) is shown.
B) Ubiquitination assay of shuffled HA-YRA1 wild-type background. The strain was transformed with a cupper inducible His-Ubiquitin expressing 2µ plasmid. His-Ubiquitin was induced with cupper over night. Cells were arrested in G1 with αFactor, irradiated (IR= 50γ) or not, and released in URA-/2%Glu medium. Samples were collected 30’, 60’, 90’ after release. His-Ubiquitinated proteins were affinity-purified and the Ubiquitinated forms of Yra1 detected by Western Blot with an αHA antibody. Western Blot of input samples with αHA antibody or with αSsn6 was used to assess input levels respectively for Yra1 and Ssn6. Experiment performed by Evelina Tutucci.
Supplementary Figure 3: Yra1 stabilization in ∆dia2 correlates with increased Yra1 ubiquitination.
A) Protein stability assays using metabolic depletion of GAL-HA-YRA1 in presence of the endogenous wild-type YRA1 gene in WT and Δdia2. Experiments were performed as described in Figure 1.4. The average of 3 independent experiments is shown.
B) Ubiquitination assay of shuffled HA-YRA1 in wild-type and Δdia2 background. Strain was transformed with a cupper inducible His-Ubiquitin expressing 2µ plasmid. His-Ubiquitin was induced with cupper over night. His-ubiquitinated proteins were affinity-purified and the ubiquitinated forms of Yra1 detected by Western Blot with an αHA antibody. Western Blot of input samples with αHA antibody was used to assess input levels of Yra1. Experiment performed by Evelina Tutucci.
Supplementary Figure 4: The yra1Δintron shows transcription dependent hyper-recombination phenotype that depends on the conserved C-terminal box.
Transcription dependent hyper-recombination assay: HA-YRA1 WT, HA-yra1Δintron, HA-yra1allKR, HA-yra1(1-210) (shuffled strains) and Δhpr1 (used as positive control) (Chavez et al., 2001) and WT W303 were transformed with the plasmid based reporters # 631 (pRS316L, URA3 Cen) and # 632 (pRS316LYΔNS, URA3 Cen) from the Aguilera lab (Gavalda et al., 2016). Both reporters are based on the same direct-repeats (600bp internal fragments of the LEU2 gene sharing 300bp homology transcribed from the LEU2 promoter); they differ in the length of the intervening sequence as indicated in the scheme above. Hyper-recombination between the repeats results in formation of a functional LEU2 gene and growth on LEU- medium.. For each strain, dilutions of six distinct transformed colonies were plated on URA- (1/20000 dilution) and URA-/LEU- (1/100 dilution) medium. The percentage of recombination was calculated based on the following formula: (n° of colonies on URA-/LEU-)/ (n° of colonies on URA-*200). The very high hyper-recombination rate observed in HA-yra1Δintron in presence of plasmid # 632, but not plasmid # 631, indicates that hyper-recombination is transcription-dependent. Experiment performed by Antoine Rohrbach.
References
Abruzzi, K.C., Lacadie, S., and Rosbash, M. (2004). Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes. Embo J 23, 2620-2631.
Alber, F., Dokudovskaya, S., Veenhoff, L.M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B.T., et al. (2007). The molecular architecture of the nuclear pore complex. Nature 450, 695-701.
Altmannova, V., Kolesar, P., and Krejci, L. (2012). SUMO Wrestles with Recombination. Biomolecules 2, 350-375.
Alvaro, D., Lisby, M., and Rothstein, R. (2007). Genome-wide analysis of Rad52 foci reveals diverse mechanisms impacting recombination. PLoS Genet 3, e228.
Andrulis, E.D., Zappulla, D.C., Ansari, A., Perrod, S., Laiosa, C.V., Gartenberg, M.R., and Sternglanz, R. (2002). Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Mol Cell Biol 22, 8292-8301.
Ansari, A., and Hampsey, M. (2005). A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev 19, 2969-2978.
Aymard, F., Bugler, B., Schmidt, C.K., Guillou, E., Caron, P., Briois, S., Iacovoni, J.S., Daburon, V., Miller, K.M., Jackson, S.P., et al. (2014). Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat Struct Mol Biol 21, 366-374.
Baejen, C., Torkler, P., Gressel, S., Essig, K., Soding, J., and Cramer, P. (2014).
Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Mol Cell 55, 745-757.
Barilla, D., Lee, B.A., and Proudfoot, N.J. (2001). Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 98, 445-450.
Barlow, J.H., and Rothstein, R. (2010). Timing is everything: cell cycle control of Rad52. Cell Div 5, 7.
Bayliss, R., Littlewood, T., and Stewart, M. (2000). Structural basis for the interaction between FxFG nucleoporin repeats and importin-beta in nuclear trafficking. Cell 102, 99-108.
Bentley, D.L. (2014). Coupling mRNA processing with transcription in time and space. Nat Rev Genet 15, 163-175.
Bermejo, R., Capra, T., Jossen, R., Colosio, A., Frattini, C., Carotenuto, W., Cocito, A., Doksani, Y., Klein, H., Gomez-Gonzalez, B., et al. (2011). The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores.
Cell 146, 233-246.
Bermejo, R., Lai, M.S., and Foiani, M. (2012). Preventing replication stress to maintain genome stability: resolving conflicts between replication and transcription.
Mol Cell 45, 710-718.
Blobel, G. (1985). Gene gating: a hypothesis. Proc Natl Acad Sci U S A 82, 8527-8529.
Bohm, S., Mihalevic, M.J., Casal, M.A., and Bernstein, K.A. (2015). Disruption of SUMO-targeted ubiquitin ligases Slx5-Slx8/RNF4 alters RecQ-like helicase Sgs1/BLM localization in yeast and human cells. DNA Repair (Amst) 26, 1-14.
Brickner, D.G., Cajigas, I., Fondufe-Mittendorf, Y., Ahmed, S., Lee, P.C., Widom, J., and Brickner, J.H. (2007). H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 5, e81.
Brickner, D.G., Light, W., and Brickner, J.H. (2010). Quantitative localization of chromosomal loci by immunofluorescence. Methods Enzymol 470, 569-580.
Brickner, J.H., and Walter, P. (2004). Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2, e342.
Bupp, J.M., Martin, A.E., Stensrud, E.S., and Jaspersen, S.L. (2007). Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3. J Cell Biol 179, 845-854.
Burd, C.G., and Dreyfuss, G. (1994). Conserved structures and diversity of functions of RNA-binding proteins. Science 265, 615-621.
Burgess, R.C., Rahman, S., Lisby, M., Rothstein, R., and Zhao, X. (2007). The Slx5-Slx8 complex affects sumoylation of DNA repair proteins and negatively regulates recombination. Mol Cell Biol 27, 6153-6162.
Bystricky, K., Laroche, T., van Houwe, G., Blaszczyk, M., and Gasser, S.M. (2005).
Chromosome looping in yeast: telomere pairing and coordinated movement reflect anchoring efficiency and territorial organization. J Cell Biol 168, 375-387.
Cabal, G.G., Genovesio, A., Rodriguez-Navarro, S., Zimmer, C., Gadal, O., Lesne, A., Buc, H., Feuerbach-Fournier, F., Olivo-Marin, J.C., Hurt, E.C., et al. (2006). SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope.
Nature 441, 770-773.
Callahan, K.P., and Butler, J.S. (2010). TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. J Biol Chem 285, 3540-3547.
Casolari, J.M., Brown, C.R., Drubin, D.A., Rando, O.J., and Silver, P.A. (2005).
Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 19, 1188-1198.
Castelnuovo, M., and Stutz, F. (2013). Gene loops and HDACs to promote transcription directionality. Nucleus 4, 92-94.
Caydasi, A.K., Ibrahim, B., and Pereira, G. (2010). Monitoring spindle orientation:
Spindle position checkpoint in charge. Cell Div 5, 28.
Caydasi, A.K., and Pereira, G. (2012). SPOC alert--when chromosomes get the wrong direction. Exp Cell Res 318, 1421-1427.
Chan, Y.A., Hieter, P., and Stirling, P.C. (2014). Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 30, 245-253.
Chavez, S., Beilharz, T., Rondon, A.G., Erdjument-Bromage, H., Tempst, P., Svejstrup, J.Q., Lithgow, T., and Aguilera, A. (2000). A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J 19, 5824-5834.
Chavez, S., Garcia-Rubio, M., Prado, F., and Aguilera, A. (2001). Hpr1 is preferentially required for transcription of either long or G+C-rich DNA sequences in Saccharomyces cerevisiae. Mol Cell Biol 21, 7054-7064.
Cho, E.J., Takagi, T., Moore, C.R., and Buratowski, S. (1997). mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev 11, 3319-3326.
Christiano, R., Nagaraj, N., Frohlich, F., and Walther, T.C. (2014). Global proteome turnover analyses of the Yeasts S. cerevisiae and S. pombe. Cell Rep 9, 1959-1965.
Chung, I., and Zhao, X. (2015). DNA break-induced sumoylation is enabled by collaboration between a SUMO ligase and the ssDNA-binding complex RPA. Genes Dev 29, 1593-1598.
Churikov, D., Charifi, F., Eckert-Boulet, N., Silva, S., Simon, M.N., Lisby, M., and Geli, V. (2016). SUMO-Dependent Relocalization of Eroded Telomeres to Nuclear Pore Complexes Controls Telomere Recombination. Cell Rep 15, 1242-1253.
Cook, C.E., Hochstrasser, M., and Kerscher, O. (2009). The SUMO-targeted ubiquitin ligase subunit Slx5 resides in nuclear foci and at sites of DNA breaks. Cell Cycle 8, 1080-1089.
Corden, J.L., Cadena, D.L., Ahearn, J.M., Jr., and Dahmus, M.E. (1985). A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc Natl Acad Sci U S A 82, 7934-7938.
Cordon-Preciado, V., Ufano, S., and Bueno, A. (2006). Limiting amounts of budding yeast Rad53 S-phase checkpoint activity results in increased resistance to DNA alkylation damage. Nucleic Acids Res 34, 5852-5862.
Cosma, M.P. (2004). Daughter-specific repression of Saccharomyces cerevisiae HO:
Ash1 is the commander. EMBO Rep 5, 953-957.
Cremona, C.A., Sarangi, P., Yang, Y., Hang, L.E., Rahman, S., and Zhao, X. (2012).
Extensive DNA damage-induced sumoylation contributes to replication and repair and acts in addition to the mec1 checkpoint. Mol Cell 45, 422-432.
Crick, F. (1970). Central dogma of molecular biology. Nature 227, 561-563.
Cronshaw, J.M., Krutchinsky, A.N., Zhang, W., Chait, B.T., and Matunis, M.J. (2002).
Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol 158, 915-927.
D'Angelo, M.A., and Hetzer, M.W. (2008). Structure, dynamics and function of nuclear pore complexes. Trends Cell Biol 18, 456-466.
Das, S., and Das, B. (2013). mRNA quality control pathways in Saccharomyces cerevisiae. J Biosci 38, 615-640.
DeGrasse, J.A., DuBois, K.N., Devos, D., Siegel, T.N., Sali, A., Field, M.C., Rout, M.P., and Chait, B.T. (2009). Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol Cell Proteomics 8, 2119-2130.
Dermody, J.L., Dreyfuss, J.M., Villen, J., Ogundipe, B., Gygi, S.P., Park, P.J., Ponticelli, A.S., Moore, C.L., Buratowski, S., and Bucheli, M.E. (2008).
Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation.
PLoS One 3, e3273.
Dichtl, B., Blank, D., Sadowski, M., Hubner, W., Weiser, S., and Keller, W. (2002).
Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination. EMBO J 21, 4125-4135.
Dieppois, G., Iglesias, N., and Stutz, F. (2006). Cotranscriptional recruitment to the mRNA export receptor Mex67p contributes to nuclear pore anchoring of activated genes. Mol Cell Biol 26, 7858-7870.
Dilworth, D.J., Suprapto, A., Padovan, J.C., Chait, B.T., Wozniak, R.W., Rout, M.P., and Aitchison, J.D. (2001). Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex. J Cell Biol 153, 1465-1478.
Dion, V., Kalck, V., Horigome, C., Towbin, B.D., and Gasser, S.M. (2012). Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery. Nat Cell Biol 14, 502-509.
Dion, V., Kalck, V., Seeber, A., Schleker, T., and Gasser, S.M. (2013). Cohesin and the nucleolus constrain the mobility of spontaneous repair foci. EMBO Rep 14, 984-991.
Dong, S., Jacobson, A., and He, F. (2010a). Degradation of YRA1 Pre-mRNA in the cytoplasm requires translational repression, multiple modular intronic elements, Edc3p, and Mex67p. PLoS Biol 8, e1000360.
Dong, S., Jacobson, A., and He, F. (2010b). Degradation of YRA1 Pre-mRNA in the cytoplasm requires translational repression, multiple modular intronic elements, Edc3p, and Mex67p. PLoS Biol 8, e1000360.
Dong, S., Li, C., Zenklusen, D., Singer, R.H., Jacobson, A., and He, F. (2007a). YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol Cell 25, 559-573.
Dong, S., Li, C., Zenklusen, D., Singer, R.H., Jacobson, A., and He, F. (2007b). YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol Cell 25, 559-573.
Duan, Z., Andronescu, M., Schutz, K., McIlwain, S., Kim, Y.J., Lee, C., Shendure, J., Fields, S., Blau, C.A., and Noble, W.S. (2010). A three-dimensional model of the yeast genome. Nature 465, 363-367.
Ebrahimi, H., and Donaldson, A.D. (2008). Release of yeast telomeres from the nuclear periphery is triggered by replication and maintained by suppression of Ku-mediated anchoring. Genes Dev 22, 3363-3374.
Espinet, C., de la Torre, M.A., Aldea, M., and Herrero, E. (1995). An efficient method to isolate yeast genes causing overexpression-mediated growth arrest. Yeast 11, 25-32.
Fasken, M.B., Stewart, M., and Corbett, A.H. (2008). Functional significance of the interaction between the mRNA-binding protein, Nab2, and the nuclear pore-associated protein, Mlp1, in mRNA export. J Biol Chem 283, 27130-27143.
Fernandez-Pevida, A., Kressler, D., and de la Cruz, J. (2015). Processing of preribosomal RNA in Saccharomyces cerevisiae. Wiley Interdiscip Rev RNA 6, 191-209.
Ferreira, H.C., Luke, B., Schober, H., Kalck, V., Lingner, J., and Gasser, S.M. (2011).
The PIAS homologue Siz2 regulates perinuclear telomere position and telomerase activity in budding yeast. Nat Cell Biol 13, 867-874.
Fischer, T., Strasser, K., Racz, A., Rodriguez-Navarro, S., Oppizzi, M., Ihrig, P., Lechner, J., and Hurt, E. (2002). The mRNA export machinery requires the novel Sac3p-Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores.
EMBO J 21, 5843-5852.
Fong, C.M., Arumugam, A., and Koepp, D.M. (2013). The Saccharomyces cerevisiae F-box protein Dia2 is a mediator of S-phase checkpoint recovery from DNA damage.
Genetics 193, 483-499.
Fu, Y., Pastushok, L., and Xiao, W. (2008). DNA damage-induced gene expression in Saccharomyces cerevisiae. FEMS Microbiol Rev 32, 908-926.
Galy, V., Gadal, O., Fromont-Racine, M., Romano, A., Jacquier, A., and Nehrbass, U.
(2004). Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 116, 63-73.
Gavalda, S., Santos-Pereira, J.M., Garcia-Rubio, M.L., Luna, R., and Aguilera, A.
(2016). Excess of Yra1 RNA-Binding Factor Causes Transcription-Dependent Genome Instability, Replication Impairment and Telomere Shortening. PLoS Genet 12, e1005966.
Gilbert, W., Siebel, C.W., and Guthrie, C. (2001). Phosphorylation by Sky1p promotes Npl3p shuttling and mRNA dissociation. RNA 7, 302-313.
Gobbini, E., Cesena, D., Galbiati, A., Lockhart, A., and Longhese, M.P. (2013).
Interplays between ATM/Tel1 and ATR/Mec1 in sensing and signaling DNA double-strand breaks. DNA Repair (Amst) 12, 791-799.
Gotta, M., Laroche, T., Formenton, A., Maillet, L., Scherthan, H., and Gasser, S.M.
(1996). The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J Cell Biol 134, 1349-1363.
Grzechnik, P., Tan-Wong, S.M., and Proudfoot, N.J. (2014). Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 39, 319-327.
Gwizdek, C., Iglesias, N., Rodriguez, M.S., Ossareh-Nazari, B., Hobeika, M., Divita, G., Stutz, F., and Dargemont, C. (2006). Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A 103, 16376-16381.
Hamperl, S., and Cimprich, K.A. (2014). The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 19, 84-94.
Hediger, F., and Gasser, S.M. (2002). Nuclear organization and silencing: putting things in their place. Nat Cell Biol 4, E53-55.
Helmrich, A., Ballarino, M., Nudler, E., and Tora, L. (2013). Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol 20, 412-418.
Henriksen, P., Wagner, S.A., Weinert, B.T., Sharma, S., Bacinskaja, G., Rehman, M., Juffer, A.H., Walther, T.C., Lisby, M., and Choudhary, C. (2012). Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics 11, 1510-1522.
Herbert, S., Brion, A., Arbona, J.M., Lelek, M., Veillet, A., Lelandais, B., Parmar, J., Fernandez, F.G., Almayrac, E., Khalil, Y., et al. (2017). Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast. EMBO J.
Hickey, C.M., Wilson, N.R., and Hochstrasser, M. (2012). Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol 13, 755-766.
Hieter, P., Mann, C., Snyder, M., and Davis, R.W. (1985). Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell 40, 381-392.
Hilleren, P., McCarthy, T., Rosbash, M., Parker, R., and Jensen, T.H. (2001). Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature 413, 538-542.
Hirota, K., Tsuda, M., Murai, J., Takagi, T., Keka, I.S., Narita, T., Fujita, M., Sasanuma, H., Kobayashi, J., and Takeda, S. (2014). SUMO-targeted ubiquitin ligase RNF4 plays a critical role in preventing chromosome loss. Genes Cells 19, 743-754.
Hobeika, M., Brockmann, C., Iglesias, N., Gwizdek, C., Neuhaus, D., Stutz, F., Stewart, M., Divita, G., and Dargemont, C. (2007). Coordination of Hpr1 and ubiquitin
binding by the UBA domain of the mRNA export factor Mex67. Mol Biol Cell 18, 2561-2568.
Horigome, C., Bustard, D.E., Marcomini, I., Delgoshaie, N., Tsai-Pflugfelder, M., Cobb, J.A., and Gasser, S.M. (2016). PolySUMOylation by Siz2 and Mms21 triggers relocation of DNA breaks to nuclear pores through the Slx5/Slx8 STUbL. Genes Dev 30, 931-945.
Horigome, C., Dion, V., Seeber, A., Gehlen, L.R., and Gasser, S.M. (2015).
Visualizing the spatiotemporal dynamics of DNA damage in budding yeast. Methods Mol Biol 1292, 77-96.
Horigome, C., and Gasser, S.M. (2016). SUMO wrestles breaks to the nuclear ring's edge. Cell Cycle 15, 3011-3013.
Horigome, C., Oma, Y., Konishi, T., Schmid, R., Marcomini, I., Hauer, M.H., Dion, V., Harata, M., and Gasser, S.M. (2014). SWR1 and INO80 chromatin remodelers contribute to DNA double-strand break perinuclear anchorage site choice. Mol Cell 55, 626-639.
Hoyt, M.A., Totis, L., and Roberts, B.T. (1991). S. cerevisiae genes required for cell cycle arrest in response to loss of microtubule function. Cell 66, 507-517.
Huertas, P., and Aguilera, A. (2003). Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 12, 711-721.
Hurt, E., Luo, M.J., Rother, S., Reed, R., and Strasser, K. (2004). Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc Natl Acad Sci U S A 101, 1858-1862.
Iglesias, N., Tutucci, E., Gwizdek, C., Vinciguerra, P., Von Dach, E., Corbett, A.H., Dargemont, C., and Stutz, F. (2010). Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes Dev 24, 1927-1938.
Jackson, S.P., and Durocher, D. (2013). Regulation of DNA damage responses by ubiquitin and SUMO. Mol Cell 49, 795-807.
Jaehnig, E.J., Kuo, D., Hombauer, H., Ideker, T.G., and Kolodner, R.D. (2013).
Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep 4, 174-188.
Jani, D., Lutz, S., Marshall, N.J., Fischer, T., Kohler, A., Ellisdon, A.M., Hurt, E., and Stewart, M. (2009). Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export. Mol Cell 33, 727-737.
Jani, D., Valkov, E., and Stewart, M. (2014). Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export. Nucleic Acids Res 42, 6686-6697.
Jiao, X., Xiang, S., Oh, C., Martin, C.E., Tong, L., and Kiledjian, M. (2010).
Identification of a quality-control mechanism for mRNA 5'-end capping. Nature 467, 608-611.
Jimeno, S., Rondon, A.G., Luna, R., and Aguilera, A. (2002). The yeast THO complex and mRNA export factors link RNA metabolism with transcription and genome instability. EMBO J 21, 3526-3535.
Johnson, S.A., Cubberley, G., and Bentley, D.L. (2009a). Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11. Mol Cell 33, 215-226.
Johnson, S.A., Cubberley, G., and Bentley, D.L. (2009b). Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11. Mol Cell 33, 215-226.
Johnson, S.A., Kim, H., Erickson, B., and Bentley, D.L. (2011a). The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol 18, 1164-1171.
Johnson, S.A., Kim, H., Erickson, B., and Bentley, D.L. (2011b). The export factor Yra1 modulates mRNA 3' end processing. Nat Struct Mol Biol 18, 1164-1171.
Jossen, R., and Bermejo, R. (2013a). The DNA damage checkpoint response to replication stress: A Game of Forks. Front Genet 4, 26.
Jossen, R., and Bermejo, R. (2013b). The DNA damage checkpoint response to replication stress: A Game of Forks. Front Genet 4, 26.
Kalocsay, M., Hiller, N.J., and Jentsch, S. (2009). Chromosome-wide Rad51 spreading and SUMO-H2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break. Mol Cell 33, 335-343.
Kashyap, A.K., Schieltz, D., Yates, J., 3rd, and Kellogg, D.R. (2005). Biochemical and genetic characterization of Yra1p in budding yeast. Yeast 22, 43-56.
Katahira, J., Strasser, K., Podtelejnikov, A., Mann, M., Jung, J.U., and Hurt, E. (1999).
The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human. EMBO J 18, 2593-2609.
Keskin, H., Shen, Y., Huang, F., Patel, M., Yang, T., Ashley, K., Mazin, A.V., and Storici, F. (2014). Transcript-RNA-templated DNA recombination and repair. Nature 515, 436-439.
Khadaroo, B., Teixeira, M.T., Luciano, P., Eckert-Boulet, N., Germann, S.M., Simon, M.N., Gallina, I., Abdallah, P., Gilson, E., Geli, V., et al. (2009). The DNA damage response at eroded telomeres and tethering to the nuclear pore complex. Nat Cell Biol 11, 980-987.
Kress, T.L., Krogan, N.J., and Guthrie, C. (2008). A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Mol Cell 32, 727-734.
Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P., et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
Kupke, T., Di Cecco, L., Muller, H.M., Neuner, A., Adolf, F., Wieland, F., Nickel, W., and Schiebel, E. (2011). Targeting of Nbp1 to the inner nuclear membrane is essential for spindle pole body duplication. EMBO J 30, 3337-3352.
Kyburz, A., Sadowski, M., Dichtl, B., and Keller, W. (2003). The role of the yeast cleavage and polyadenylation factor subunit Ydh1p/Cft2p in pre-mRNA 3'-end formation. Nucleic Acids Res 31, 3936-3945.
Laine, J.P., Singh, B.N., Krishnamurthy, S., and Hampsey, M. (2009). A physiological role for gene loops in yeast. Genes Dev 23, 2604-2609.
Lebeaupin, T., Sellou, H., Timinszky, G., Huet S., et al (2015). Chromatin dynamics at DNA breaks: what, how and why? AIMS Biophysics 2(4), 458-475.
Ledoux, S., and Guthrie, C. (2011). Regulation of the Dbp5 ATPase cycle in mRNP remodeling at the nuclear pore: a lively new paradigm for DEAD-box proteins. Genes Dev 25, 1109-1114.
Leger-Silvestre, I., Trumtel, S., Noaillac-Depeyre, J., and Gas, N. (1999). Functional compartmentalization of the nucleus in the budding yeast Saccharomyces cerevisiae.
Chromosoma 108, 103-113.
Lei, E.P., Stern, C.A., Fahrenkrog, B., Krebber, H., Moy, T.I., Aebi, U., and Silver, P.A. (2003). Sac3 is an mRNA export factor that localizes to cytoplasmic fibrils of nuclear pore complex. Mol Biol Cell 14, 836-847.
Lew, D.J., and Burke, D.J. (2003). The spindle assembly and spindle position checkpoints. Annu Rev Genet 37, 251-282.
Li, R., and Murray, A.W. (1991). Feedback control of mitosis in budding yeast. Cell 66, 519-531.
Lisby, M., Mortensen, U.H., and Rothstein, R. (2003). Colocalization of multiple DNA
Lisby, M., Mortensen, U.H., and Rothstein, R. (2003). Colocalization of multiple DNA