University of Dundee

Gene Regulation and Expression 2015

 
Abdel-Fattah, W., Jablonowski, D., Di Santo, R., Thuring, K. L., Scheidt, V., Hammermeister, A., Ten Have, S., Helm, M., Schaffrath, R. and Stark, M. J. (2015) Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS genetics. 11, e1004931
d.o.i: 10.1371/journal.pgen.1004931
PubMed: 4287497
PMC: 25569479
 
Aguilar-Martinez, E., Chen, X., Webber, A., Mould, A. P., Seifert, A., Hay, R. T. and Sharrocks, A. D. (2015) Screen for multi-SUMO-binding proteins reveals a multi-SIM-binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin. Proceedings of the National Academy of Sciences of the United States of America. 112, E4854-4863
d.o.i: 10.1073/pnas.1509716112
PubMed: 4568223
PMC: 26283374
 
Alabert, C., Barth, T. K., Reveron-Gomez, N., Sidoli, S., Schmidt, A., Jensen, O. N., Imhof, A. and Groth, A. (2015) Two distinct modes for propagation of histone PTMs across the cell cycle. Genes & development. 29, 585-590
d.o.i: 10.1101/gad.256354.114
PubMed: 4378191
PMC: 25792596
 
Bailly, A., Perrin, A., Bou Malhab, L. J., Pion, E., Larance, M., Nagala, M., Smith, P., O'Donohue, M. F., Gleizes, P. E., Zomerdijk, J., Lamond, A. I. and Xirodimas, D. P. (2015) The NEDD8 inhibitor MLN4924 increases the size of the nucleolus and activates p53 through the ribosomal-Mdm2 pathway. Oncogene
d.o.i: 10.1038/onc.2015.104
PMC: 25867069
 
Bandarra, D., Biddlestone, J., Mudie, S., Muller, H. A. and Rocha, S. (2015) HIF-1alpha restricts NF-kappaB-dependent gene expression to control innate immunity signals. Disease models & mechanisms. 8, 169-181
d.o.i: 10.1242/dmm.017285
PubMed: 4314782
PMC: 25510503
 
Bensaddek, D., Narayan, V., Nicolas, A., Murillo, A. B., Gartner, A., Kenyon, C. J. and Lamond, A. I. (2016) Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics. 16, 381-392
d.o.i: 10.1002/pmic.201500264
PubMed: 4819713
PMC: 26552604
 
Bensaddek, D., Nicolas, A. and Lamond, A. I. (2015) Evaluating the use of HILIC in large-scale, multi dimensional proteomics: Horses for courses? International journal of mass spectrometry. 391, 105-114
d.o.i: 10.1016/j.ijms.2015.07.029
PubMed: 4708065
PMC: 26869852
 
Bett, J. S., Ritorto, M. S., Ewan, R., Jaffray, E. G., Virdee, S., Chin, J. W., Knebel, A., Kurz, T., Trost, M., Tatham, M. H. and Hay, R. T. (2015) Ubiquitin C-terminal hydrolases cleave isopeptide- and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers. The Biochemical journal. 466, 489-498
d.o.i: 10.1042/BJ20141349
PubMed: 4353193
PMC: 25489924
 
Biddlestone, J., Bandarra, D. and Rocha, S. (2015) The role of hypoxia in inflammatory disease (review). International journal of molecular medicine. 35, 859-869
d.o.i: 10.3892/ijmm.2015.2079
PubMed: 4356629
PMC: 25625467
 
Branigan, E., Plechanovova, A., Jaffray, E. G., Naismith, J. H. and Hay, R. T. (2015) Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains. Nature structural & molecular biology. 22, 597-602
d.o.i: 10.1038/nsmb.3052
PubMed: 4529489
PMC: 26148049
 
Burel, J. M., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Li, S., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczysko, P., Allan, C., Moore, J. and Swedlow, J. R. (2015) Publishing and sharing multi-dimensional image data with OMERO. Mammalian genome : official journal of the International Mammalian Genome Society. 26, 441-447
d.o.i: 10.1007/s00335-015-9587-6
PubMed: 4602067
PMC: 26223880
 
Domingues, P., Golebiowski, F., Tatham, M. H., Lopes, A. M., Taggart, A., Hay, R. T. and Hale, B. G. (2015) Global Reprogramming of Host SUMOylation during Influenza Virus Infection. Cell reports. 13, 1467-1480
d.o.i: 10.1016/j.celrep.2015.10.001
PubMed: 4660286
PMC: 26549460
 
Drozdetskiy, A., Cole, C., Procter, J. and Barton, G. J. (2015) JPred4: a protein secondary structure prediction server. Nucleic acids research. 43, W389-394
d.o.i: 10.1093/nar/gkv332
PubMed: 4489285
PMC: 25883141
 
Dunn, S. and Cowling, V. H. (2015) Myc and mRNA capping. Biochimica et biophysica acta. 1849, 501-505
d.o.i: 10.1016/j.bbagrm.2014.03.007
PubMed: PMC: 24681440
 
Fray, R. G. and Simpson, G. G. (2015) The Arabidopsis epitranscriptome. Curr Opin Plant Biol. 27, 17-21
d.o.i: 10.1016/j.pbi.2015.05.015
PubMed: PMC: 26048078
 
Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. and Barton, G. J. (2015) Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. Bioinformatics. 31, 3625-3630
d.o.i: 10.1093/bioinformatics/btv425
PubMed: 4754627
PMC: 26206307
 
Hutten, S., Swift, S. and Lamond, A. I. (2015) Time-lapse imaging of nuclear bodies. Methods in molecular biology. 1262, 55-67
d.o.i: 10.1007/978-1-4939-2253-6_4
PMC: 25555575
 
Ibrahim-Verbaas, C. A., Bressler, J., Debette, S., Schuur, M., Smith, A. V., Bis, J. C., Davies, G., Trompet, S., Smith, J. A., Wolf, C., Chibnik, L. B., Liu, Y., Vitart, V., Kirin, M., Petrovic, K., Polasek, O., Zgaga, L., Fawns-Ritchie, C., Hoffmann, P., Karjalainen, J., Lahti, J., Llewellyn, D. J., Schmidt, C. O., Mather, K. A., Chouraki, V., Sun, Q., Resnick, S. M., Rose, L. M., Oldmeadow, C., Stewart, M., Smith, B. H., Gudnason, V., Yang, Q., Mirza, S. S., Jukema, J. W., deJager, P. L., Harris, T. B., Liewald, D. C., Amin, N., Coker, L. H., Stegle, O., Lopez, O. L., Schmidt, R., Teumer, A., Ford, I., Karbalai, N., Becker, J. T., Jonsdottir, M. K., Au, R., Fehrmann, R. S., Herms, S., Nalls, M., Zhao, W., Turner, S. T., Yaffe, K., Lohman, K., van Swieten, J. C., Kardia, S. L., Knopman, D. S., Meeks, W. M., Heiss, G., Holliday, E. G., Schofield, P. W., Tanaka, T., Stott, D. J., Wang, J., Ridker, P., Gow, A. J., Pattie, A., Starr, J. M., Hocking, L. J., Armstrong, N. J., McLachlan, S., Shulman, J. M., Pilling, L. C., Eiriksdottir, G., Scott, R. J., Kochan, N. A., Palotie, A., Hsieh, Y. C., Eriksson, J. G., Penman, A., Gottesman, R. F., Oostra, B. A., Yu, L., DeStefano, A. L., Beiser, A., Garcia, M., Rotter, J. I., Nothen, M. M., Hofman, A., Slagboom, P. E., Westendorp, R. G., Buckley, B. M., Wolf, P. A., Uitterlinden, A. G., Psaty, B. M., Grabe, H. J., Bandinelli, S., Chasman, D. I., Grodstein, F., Raikkonen, K., Lambert, J. C., Porteous, D. J., Generation, S., Price, J. F., Sachdev, P. S., Ferrucci, L., Attia, J. R., Rudan, I., Hayward, C., Wright, A. F., Wilson, J. F., Cichon, S., Franke, L., Schmidt, H., Ding, J., de Craen, A. J., Fornage, M., Bennett, D. A., Deary, I. J., Ikram, M. A., Launer, L. J., Fitzpatrick, A. L., Seshadri, S., van Duijn, C. M. and Mosley, T. H. (2016) GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Molecular psychiatry. 21, 189-197
d.o.i: 10.1038/mp.2015.37
PubMed: 4722802
PMC: 25869804
 
Judes, A., Ebert, F., Bar, C., Thuring, K. L., Harrer, A., Klassen, R., Helm, M., Stark, M. J. and Schaffrath, R. (2015) Urmylation and tRNA thiolation functions of ubiquitin-like Uba4.Urm1 systems are conserved from yeast to man. FEBS Lett. 589, 904-909
d.o.i: 10.1016/j.febslet.2015.02.024
PMC: 25747390
 
Kalantzaki, M., Kitamura, E., Zhang, T., Mino, A., Novak, B. and Tanaka, T. U. (2015) Kinetochore-microtubule error correction is driven by differentially regulated interaction modes. Nature cell biology. 17, 421-433
d.o.i: 10.1038/ncb3128
PubMed: 4380510
PMC: 25751138
 
Kobayashi, N., Suzuki, Y., Schoenfeld, L. W., Muller, C. A., Nieduszynski, C., Wolfe, K. H. and Tanaka, T. U. (2015) Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. Current biology : CB. 25, 2026-2033
d.o.i: 10.1016/j.cub.2015.06.023
PubMed: 4533239
PMC: 26166782
 
Kohler, J. B., Tammsalu, T., Jorgensen, M. M., Steen, N., Hay, R. T. and Thon, G. (2015) Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast. Nature communications. 6, 8827
d.o.i: 10.1038/ncomms9827
PubMed: 4667616
PMC: 26537787
 
Larance, M. and Lamond, A. I. (2015) Multidimensional proteomics for cell biology. Nature reviews. Molecular cell biology. 16, 269-280
d.o.i: 10.1038/nrm3970
PMC: 25857810
 
Larance, M., Pourkarimi, E., Wang, B., Brenes Murillo, A., Kent, R., Lamond, A. I. and Gartner, A. (2015) Global Proteomics Analysis of the Response to Starvation in C. elegans. Molecular & cellular proteomics : MCP. 14, 1989-2001
d.o.i: 10.1074/mcp.M114.044289
PubMed: 4587315
PMC: 25963834
 
Liu, Y., Freeman, A. D., Declais, A. C., Wilson, T. J., Gartner, A. and Lilley, D. M. (2015) Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA. Cell reports. 13, 2565-2575
d.o.i: 10.1016/j.celrep.2015.11.042
PubMed: 4695337
PMC: 26686639
 
Ly, T., Endo, A. and Lamond, A. I. (2015) Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells. eLife. 4
d.o.i: 10.7554/eLife.04534
PubMed: 4383314
PMC: 25555159
 
Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. and Barton, G. J. (2015) 14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics
d.o.i: 10.1093/bioinformatics/btv133
PMC: 25735772
 
Mariappa, D., Zheng, X., Schimpl, M., Raimi, O., Ferenbach, A. T., Muller, H. A. and van Aalten, D. M. (2015) Dual functionality of O-GlcNAc transferase is required for Drosophila development. Open biology. 5, 150234
d.o.i: 10.1098/rsob.150234
PubMed: 4703063
PMC: 26674417
 
Masuzzo, P., Martens, L., Cell Migration Workshop, P., Ampe, C., Anderson, K. I., Barry, J., De Wever, O., Debeir, O., Decaestecker, C., Dolznig, H., Friedl, P., Gaggioli, C., Geiger, B., Goldberg, I. G., Horn, E., Horwitz, R., Kam, Z., Le Devedec, S. E., Vignjevic, D. M., Moore, J., Olivo-Marin, J. C., Sahai, E., Sansone, S. A., Sanz-Moreno, V., Stromblad, S., Swedlow, J., Textor, J., Van Troys, M. and Zantl, R. (2015) An open data ecosystem for cell migration research. Trends Cell Biol. 25, 55-58
d.o.i: 10.1016/j.tcb.2014.11.005
PMC: 25484346
 
Moniz, S., Bandarra, D., Biddlestone, J., Campbell, K. J., Komander, D., Bremm, A. and Rocha, S. (2015) Cezanne regulates E2F1-dependent HIF2alpha expression. Journal of cell science. 128, 3082-3093
d.o.i: 10.1242/jcs.168864
PubMed: 4541044
PMC: 26148512
 
Moore, J., Linkert, M., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gilen, K., Leigh, R., Li, S., Lindner, D., Moore, W. J., Patterson, A. J., Pindelski, B., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczyko, P., Allan, C., Burel, J. M. and Swedlow, J. R. (2015) OMERO and Bio-Formats 5: Flexible, Scaleable, Access and Management for Large Bioimaging Dataset. SPIR Proc. 9413, 07
 
Moser, S. C., Bensaddek, D., Ortmann, B., Rocha, S., Lamond, A. I. and Swedlow, J. R. (2015) The Prolylhydroxylase PHD2 Modulates Centromere Function through the Hydroxylation of CENP-N. bioRxiv
d.o.i: 10.1101/030452
 
Ono, M., Yamada, K., Avolio, F., Afzal, V., Bensaddek, D. and Lamond, A. I. (2015) Targeted Knock-Down of miR21 Primary Transcripts Using snoMEN Vectors Induces Apoptosis in Human Cancer Cell Lines. PloS one. 10, e0138668
d.o.i: 10.1371/journal.pone.0138668
PubMed: 4583369
PMC: 26405811
 
Pathak, S., Alonso, J., Schimpl, M., Rafie, K., Blair, D. E., Borodkin, V. S., Schuttelkopf, A. W., Albarbarawi, O. and van Aalten, D. M. (2015) The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nature structural & molecular biology. 22, 744-750
d.o.i: 10.1038/nsmb.3063
PubMed: 4979681
PMC: 26237509
 
Pelisch, F., Sonneville, R., Pourkarimi, E., Agostinho, A., Blow, J. J., Gartner, A. and Hay, R. T. (2015) Erratum: Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans. Nature communications. 6, 6352
d.o.i: 10.1038/ncomms7352
PMC: 25672768
 
Preston, G. C., Sinclair, L. V., Kaskar, A., Hukelmann, J. L., Navarro, M. N., Ferrero, I., MacDonald, H. R., Cowling, V. H. and Cantrell, D. A. (2015) Single cell tuning of Myc expression by antigen receptor signal strength and interleukin-2 in T lymphocytes. The EMBO journal. 34, 2008-2024
d.o.i: 10.15252/embj.201490252
PubMed: 4551349
PMC: 26136212
 
Rojas-Fernandez, A., Herhaus, L., Macartney, T., Lachaud, C., Hay, R. T. and Sapkota, G. P. (2015) Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9. Scientific reports. 5, 9811
d.o.i: 10.1038/srep09811
PubMed: 4413877
PMC: 25922883
 
Schurch, N. C., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. and Barton, G. J. (2015) Evaluation of tools for differential gene expression analysis by RNA-seq on a 48 biological replicate experiment. arXiv. 1505, 0217
 
Seifert, A., Schofield, P., Barton, G. J. and Hay, R. T. (2015) Proteotoxic stress reprograms the chromatin landscape of SUMO modification. Science signaling. 8, rs7
d.o.i: 10.1126/scisignal.aaa2213
PMC: 26152697
 
Shlien, A., Campbell, B. B., de Borja, R., Alexandrov, L. B., Merico, D., Wedge, D., Van Loo, P., Tarpey, P. S., Coupland, P., Behjati, S., Pollett, A., Lipman, T., Heidari, A., Deshmukh, S., Avitzur, N., Meier, B., Gerstung, M., Hong, Y., Merino, D. M., Ramakrishna, M., Remke, M., Arnold, R., Panigrahi, G. B., Thakkar, N. P., Hodel, K. P., Henninger, E. E., Goksenin, A. Y., Bakry, D., Charames, G. S., Druker, H., Lerner-Ellis, J., Mistry, M., Dvir, R., Grant, R., Elhasid, R., Farah, R., Taylor, G. P., Nathan, P. C., Alexander, S., Ben-Shachar, S., Ling, S. C., Gallinger, S., Constantini, S., Dirks, P., Huang, A., Scherer, S. W., Grundy, R. G., Durno, C., Aronson, M., Gartner, A., Meyn, M. S., Taylor, M. D., Pursell, Z. F., Pearson, C. E., Malkin, D., Futreal, P. A., Stratton, M. R., Bouffet, E., Hawkins, C., Campbell, P. J., Tabori, U. and Biallelic Mismatch Repair Deficiency, C. (2015) Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nature genetics. 47, 257-262
d.o.i: 10.1038/ng.3202
PMC: 25642631
 
Sloan, E., Tatham, M. H., Groslambert, M., Glass, M., Orr, A., Hay, R. T. and Everett, R. D. (2015) Analysis of the SUMO2 Proteome during HSV-1 Infection. PLoS pathogens. 11, e1005059
d.o.i: 10.1371/journal.ppat.1005059
PubMed: 4511656
PMC: 26200910
 
Sonneville, R., Craig, G., Labib, K., Gartner, A. and Blow, J. J. (2015) Both Chromosome Decondensation and Condensation Are Dependent on DNA Replication in C. elegans Embryos. Cell reports. 12, 405-417
d.o.i: 10.1016/j.celrep.2015.06.046
PubMed: 4521082
PMC: 26166571
 
Staiger, D. and Simpson, G. G. (2015) Enter exitrons. Genome biology. 16, 136
d.o.i: 10.1186/s13059-015-0704-3
PubMed: 4494720
PMC: 26149172
 
Sun, Y., George, J. and Rocha, S. (2015) Dose-dependent effects of allopurinol on human foreskin fibroblast cells and human umbilical vein endothelial cells under hypoxia. PloS one. 10, e0123649
d.o.i: 10.1371/journal.pone.0123649
PubMed: 4382188
PMC: 25830774
 
Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F., Tatham, M. H. and Hay, R. T. (2015) Proteome-wide identification of SUMO modification sites by mass spectrometry. Nature protocols. 10, 1374-1388
d.o.i: 10.1038/nprot.2015.095
PMC: 26292070
 
Varshney, D., Vavrova-Anderson, J., Oler, A. J., Cowling, V. H., Cairns, B. R. and White, R. J. (2015) SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nature communications. 6, 6569
d.o.i: 10.1038/ncomms7569
PubMed: 4382998
PMC: 25798578
 
Wimmer, P., Berscheminski, J., Blanchette, P., Groitl, P., Branton, P. E., Hay, R. T., Dobner, T. and Schreiner, S. (2015) PML isoforms IV and V contribute to adenovirus-mediated oncogenic transformation by functionally inhibiting the tumor-suppressor p53. Oncogene
d.o.i: 10.1038/onc.2015.63
PMC: 25772236