University of Dundee

Gene Regulation and Expression 2013

Abdel-Fattah, W., Scheidt, V., Uthman, S., Stark, M. J. and Schaffrath, R. (2013) Insights into diphthamide, key diphtheria toxin effector. Toxins (Basel). 5, 958-968
doi. 10.3390/toxins5050958
Pubmed. 23645155

Agostinho, A., Meier, B., Sonneville, R., Jagut, M., Woglar, A., Blow, J., Jantsch, V. and Gartner, A. (2013) Combinatorial regulation of meiotic holliday junction resolution in C. elegans by HIM-6 (BLM) helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases. PLoS Genet. 9, e1003591
doi. 10.1371/journal.pgen.1003591
Pubmed. 23901331

Ahmad, Y. and Lamond, A. I. (2013) A perspective on proteomics in cell biology. Trends Cell Biol
doi. 10.1016/j.tcb.2013.10.010
Pubmed. 24284280

Akay, A., Craig, A., Lehrbach, N., Larance, M., Pourkarimi, E., Wright, J. E., Lamond, A., Miska, E. and Gartner, A. (2013) RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biol. 3, 130151
doi. 10.1098/rsob.130151
Pubmed. 24258276

Bailly, A. and Gartner, A. (2013) Germ cell apoptosis and DNA damage responses. Adv Exp Med Biol. 757, 249-276
doi. 10.1007/978-1-4614-4015-4_9
Pubmed. 22872480

Beck, J., Maerki, S., Posch, M., Metzger, T., Persaud, A., Scheel, H., Hofmann, K., Rotin, D., Pedrioli, P., Swedlow, J. R., Peter, M. and Sumara, I. (2013) Ubiquitylation-dependent localization of PLK1 in mitosis. Nat Cell Biol. 15, 430-439
doi. 10.1038/ncb2695
Pubmed. 23455478

Bett, J. S., Ibrahim, A. F., Garg, A. K., Kelly, V., Pedrioli, P., Rocha, S. and Hay, R. T. (2013) The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability. Biochem J. 451, 185-194
doi. 10.1042/BJ20130026
Pubmed. 23398456

Duran, R. V., MacKenzie, E. D., Boulahbel, H., Frezza, C., Heiserich, L., Tardito, S., Bussolati, O., Rocha, S., Hall, M. N. and Gottlieb, E. (2013) HIF-independent role of prolyl hydroxylases in the cellular response to amino acids. Oncogene. 32, 4549-4556
doi. 10.1038/onc.2012.465
Pubmed. 23085753

Earnshaw, W. C., Allshire, R. C., Black, B. E., Bloom, K., Brinkley, B. R., Brown, W., Cheeseman, I. M., Choo, K. H., Copenhaver, G. P., Deluca, J. G., Desai, A., Diekmann, S., Erhardt, S., Fitzgerald-Hayes, M., Foltz, D., Fukagawa, T., Gassmann, R., Gerlich, D. W., Glover, D. M., Gorbsky, G. J., Harrison, S. C., Heun, P., Hirota, T., Jansen, L. E., Karpen, G., Kops, G. J., Lampson, M. A., Lens, S. M., Losada, A., Luger, K., Maiato, H., Maddox, P. S., Margolis, R. L., Masumoto, H., McAinsh, A. D., Mellone, B. G., Meraldi, P., Musacchio, A., Oegema, K., O'Neill, R. J., Salmon, E. D., Scott, K. C., Straight, A. F., Stukenberg, P. T., Sullivan, B. A., Sullivan, K. F., Sunkel, C. E., Swedlow, J. R., Walczak, C. E., Warburton, P. E., Westermann, S., Willard, H. F., Wordeman, L., Yanagida, M., Yen, T. J., Yoda, K. and Cleveland, D. W. (2013) Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res. 21, 101-106
doi. 10.1007/s10577-013-9347-y
Pubmed. 23580138

Elcombe, C. R., Peffer, R. C., Wolf, D. C., Bailey, J., Bars, R., Bell, D., Cattley, R. C., Ferguson, S. S., Geter, D., Goetz, A., Goodman, J. I., Hester, S., Jacobs, A., Omiecinski, C. J., Schoeny, R., Xie, W. and Lake, B. G. (2013) Mode of action and human relevance analysis for nuclear receptor-mediated liver toxicity: A case study with phenobarbital as a model constitutive androstane receptor (CAR) activator. Crit Rev Toxicol
doi. 10.3109/10408444.2013.835786
Pubmed. 24180433

Gartner, A. and Akay, A. (2013) Stress Response: Anything that Doesn't Kill You Makes You Stronger. Curr Biol. 23, R1012-1014
doi. 10.1016/j.cub.2013.09.036
Pubmed. 24262828

Hawkins, M., Retkute, R., Muller, C. A., Saner, N., Tanaka, T. U., de Moura, A. P. and Nieduszynski, C. A. (2013) High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Rep. 5, 1132-1141
doi. 10.1016/j.celrep.2013.10.014
Pubmed. 24210825

Hay, R. T. (2013) Decoding the SUMO signal. Biochem Soc Trans. 41, 463-473
doi. 10.1042/BST20130015
Pubmed. 23514139

Hodge, K., Have, S. T., Hutton, L. and Lamond, A. I. (2013) Cleaning up the masses: exclusion lists to reduce contamination with HPLC-MS/MS. J Proteomics. 88, 92-103
doi. 10.1016/j.jprot.2013.02.023
Pubmed. 23501838

Kenneth, N. S., Mudie, S., Naron, S. and Rocha, S. (2013) TfR1 interacts with the IKK complex and is involved in IKK-NF-kappaB signalling. Biochem J. 449, 275-284
doi. 10.1042/BJ20120625
Pubmed. 23016877

Kirkwood, K. J., Ahmad, Y., Larance, M. and Lamond, A. I. (2013) Characterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics. Mol Cell Proteomics. 12, 3851-3873
doi. 10.1074/mcp.M113.032367
Pubmed. 24043423

Larance, M., Ahmad, Y., Kirkwood, K. J., Ly, T. and Lamond, A. I. (2013) Global subcellular characterization of protein degradation using quantitative proteomics. Mol Cell Proteomics. 12, 638-650
doi. 10.1074/mcp.M112.024547
Pubmed. 23242552

Lewandowska, D., ten Have, S., Hodge, K., Tillemans, V., Lamond, A. I. and Brown, J. W. (2013) Plant SILAC: stable-isotope labelling with amino acids of arabidopsis seedlings for quantitative proteomics. PLoS One. 8, e72207
doi. 10.1371/journal.pone.0072207
Pubmed. 23977254

Mariappa, D., Pathak, S. and van Aalten, D. M. (2013) A sweet TET-a-tete-synergy of TET proteins and O-GlcNAc transferase in transcription. Embo J. 32, 612-613
doi. 10.1038/emboj.2013.26
Pubmed. 23403924

Masoudi, N., Fancsalszky, L., Pourkarimi, E., Vellai, T., Alexa, A., Remenyi, A., Gartner, A., Mehta, A. and Takacs-Vellai, K. (2013) The NM23-H1/H2 homolog NDK-1 is required for full activation of Ras signaling in C. elegans. Development. 140, 3486-3495
doi. 10.1242/dev.094011
Pubmed. 23900546

Moser, S. C., Bensaddek, D., Ortmann, B., Maure, J. F., Mudie, S., Blow, J. J., Lamond, A. I., Swedlow, J. R. and Rocha, S. (2013) PHD1 links cell-cycle progression to oxygen sensing through hydroxylation of the centrosomal protein Cep192. Dev Cell. 26, 381-392
doi. 10.1016/j.devcel.2013.06.014
Pubmed. 23932902

Natsume, T., Muller, C. A., Katou, Y., Retkute, R., Gierlinski, M., Araki, H., Blow, J. J., Shirahige, K., Nieduszynski, C. A. and Tanaka, T. U. (2013) Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment. Mol Cell. 50, 661-674
doi. 10.1016/j.molcel.2013.05.011
Pubmed. 23746350

Ono, M., Yamada, K., Endo, A., Avolio, F. and Lamond, A. I. (2013) Analysis of human protein replacement stable cell lines established using snoMEN-PR vector. PLoS One. 8, e62305
doi. 10.1371/journal.pone.0062305
Pubmed. 23638031

Porter, I. M., Schleicher, K., Porter, M. and Swedlow, J. R. (2013) Bod1 regulates protein phosphatase 2A at mitotic kinetochores. Nat Commun. 4, 2677
doi. 10.1038/ncomms3677
Pubmed. 24157919

Pourkarimi, E. and Gartner, A. (2013) If you don't want them shed them. Cell Res. 23, 171-172
doi. 10.1038/cr.2012.121
Pubmed. 22907666

Ray, S., Panova, T., Miller, G., Volkov, A., Porter, A. C., Russell, J., Panov, K. I. and Zomerdijk, J. C. (2013) Topoisomerase IIalpha promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation. Nat Commun. 4, 1598
doi. 10.1038/ncomms2599
Pubmed. 23511463

Saner, N., Karschau, J., Natsume, T., Gierlinski, M., Retkute, R., Hawkins, M., Nieduszynski, C. A., Blow, J. J., de Moura, A. P. and Tanaka, T. U. (2013) Stochastic association of neighboring replicons creates replication factories in budding yeast. J Cell Biol. 202, 1001-1012
doi. 10.1083/jcb.201306143
Pubmed. 24062338

Sobala, A. and Hutvagner, G. (2013) Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells. RNA Biol. 10, 553-563
doi. 10.4161/rna.24285
Pubmed. 23563448

Swedlow, J. R. (2013) At the (kineto)chore, yeast really are like people. Cell. 154, 959-961
doi. 10.1016/j.cell.2013.08.012
Pubmed. 23993089

Swedlow, J. R. (2013) Quantitative fluorescence microscopy and image deconvolution. Methods Cell Biol. 114, 407-426
doi. 10.1016/B978-0-12-407761-4.00017-8
Pubmed. 23931516

Tanaka, T. U., Clayton, L. and Natsume, T. (2013) Three wise centromere functions: see no error, hear no break, speak no delay. EMBO Rep. 14, 1073-1083
doi. 10.1038/embor.2013.181
Pubmed. 24232185

Tatham, M. H., Plechanovova, A., Jaffray, E. G., Salmen, H. and Hay, R. T. (2013) Ube2W conjugates ubiquitin to alpha-amino groups of protein N-termini. Biochem J. 453, 137-145
doi. 10.1042/BJ20130244
Pubmed. 23560854

Urbaniak, M. D., Martin, D. M. and Ferguson, M. A. (2013) Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. J Proteome Res. 12, 2233-2244
doi. 10.1021/pr400086y
Pubmed. 23485197

Uthman, S., Bar, C., Scheidt, V., Liu, S., ten Have, S., Giorgini, F., Stark, M. J. and Schaffrath, R. (2013) The amidation step of diphthamide biosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5 interaction network. PLoS Genet. 9, e1003334
doi. 10.1371/journal.pgen.1003334
Pubmed. 23468660

Visvanathan, A., Ahmed, K., Even-Faitelson, L., Lleres, D., Bazett-Jones, D. P. and Lamond, A. I. (2013) Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations. PLoS One. 8, e67689
doi. 10.1371/journal.pone.0067689
Pubmed. 23840764

Yamada, K., Ono, M., Bensaddek, D., Lamond, A. I. and Rocha, S. (2013) FMN2 is a novel regulator of the cyclin-dependent kinase inhibitor p21. Cell Cycle. 12, 2348-2354
doi. 10.4161/cc.25511
Pubmed. 23839046

Yamada, K., Ono, M., Perkins, N. D., Rocha, S. and Lamond, A. I. (2013) Identification and functional characterization of FMN2, a regulator of the cyclin-dependent kinase inhibitor p21. Mol Cell. 49, 922-933
doi. 10.1016/j.molcel.2012.12.023
Pubmed. 23375502

Zomerdijk, J. (2013) Structural biology: Pivotal findings for a transcription machine. Nature. 502, 629-630
doi. 10.1038/nature12700
Pubmed. 24153180