University of Dundee

Gene Regulation and Expression 2011

Ahmad, Y., Boisvert, F. M., Lundberg, E., Uhlen, M. and Lamond, A. I. (2012) Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization. Mol Cell Proteomics. 11, M111 013680
doi. 10.1074/mcp.M111.013680
Pubmed. 22002106

Albert, B., Leger-Silvestre, I., Normand, C., Ostermaier, M. K., Perez-Fernandez, J., Panov, K. I., Zomerdijk, J. C., Schultz, P. and Gadal, O. (2011) RNA polymerase I-specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle. J Cell Biol. 192, 277-293
doi. 10.1083/jcb.201006040
Pubmed. 21263028

Blow, J. J., Ge, X. Q. and Jackson, D. A. (2011) How dormant origins promote complete genome replication. Trends Biochem Sci. 36, 405-414
doi. 10.1016/j.tibs.2011.05.002
Pubmed. 21641805

Boisvert, F. M., Ahmad, Y., Gierlinski, M., Charriere, F., Lamont, D., Scott, M., Barton, G. and Lamond, A. I. (2012) A quantitative spatial proteomics analysis of proteome turnover in human cells. Mol Cell Proteomics. 11, M111 011429
doi. 10.1074/mcp.M111.011429
Pubmed. 21937730

Bowman, A., Ward, R., Wiechens, N., Singh, V., El-Mkami, H., Norman, D. G. and Owen-Hughes, T. (2011) The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation. Mol Cell. 41, 398-408
doi. 10.1016/j.molcel.2011.01.025
Pubmed. 21329878

Bruderer, R., Tatham, M. H., Plechanovova, A., Matic, I., Garg, A. K. and Hay, R. T. (2011) Purification and identification of endogenous polySUMO conjugates. EMBO Rep. 12, 142-148
doi. 10.1038/embor.2010.206
Pubmed. 21252943

Gkikopoulos, T., Singh, V., Tsui, K., Awad, S., Renshaw, M. J., Scholfield, P., Barton, G. J., Nislow, C., Tanaka, T. U. and Owen-Hughes, T. (2011) The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. Embo J. 30, 1919-1927
doi. 10.1038/emboj.2011.112
Pubmed. 21505420

Hattersley, N., Shen, L., Jaffray, E. G. and Hay, R. T. (2011) The SUMO protease SENP6 is a direct regulator of PML nuclear bodies. Mol Biol Cell. 22, 78-90
doi. 10.1091/mbc.E10-06-0504
Pubmed. 21148299

Hutten, S., Prescott, A., James, J., Riesenberg, S., Boulon, S., Lam, Y. W. and Lamond, A. I. (2011) An intranucleolar body associated with rDNA. Chromosoma. 120, 481-499
doi. 10.1007/s00412-011-0327-8
Pubmed. 21698343

Klotz-Noack, K. and Blow, J. J. (2011) A role for dormant origins in tumor suppression. Mol Cell. 41, 495-496
doi. 10.1016/j.molcel.2011.02.014
Pubmed. 21362544

Kubota, T., Hiraga, S., Yamada, K., Lamond, A. I. and Donaldson, A. D. (2011) Quantitative proteomic analysis of chromatin reveals that Ctf18 acts in the DNA replication checkpoint. Mol Cell Proteomics. 10, M110 005561
doi. 10.1074/mcp.M110.005561
Pubmed. 21505101

Kundu, L. R., Seki, M., Watanabe, N., Murofushi, H., Furukohri, A., Waga, S., Score, A. J., Blow, J. J., Horikoshi, M., Enomoto, T. and Tada, S. (2011) Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication. Biochim Biophys Acta. 1813, 1129-1136
doi. 10.1016/j.bbamcr.2011.01.002
Pubmed. 21232560

Larance, M., Bailly, A. P., Pourkarimi, E., Hay, R. T., Buchanan, G., Coulthurst, S., Xirodimas, D. P., Gartner, A. and Lamond, A. I. (2011) Stable-isotope labeling with amino acids in nematodes. Nat Methods. 8, 849-851
doi. 10.1038/nmeth.1679
Pubmed. 21874007

Cruvinel Neto, J. and Dedivitis, R. A. (2011) [Prognostic factors of penetrating neck trauma]. Braz J Otorhinolaryngol. 77, 121-124
Pubmed. 21340200

Culver, C., Melvin, A., Mudie, S. and Rocha, S. (2011) HIF-1alpha depletion results in SP1-mediated cell cycle disruption and alters the cellular response to chemotherapeutic drugs. Cell Cycle. 10, 1249-1260
Pubmed. 21412054

Dellago, H., Loscher, M., Ajuh, P., Ryder, U., Kaisermayer, C., Grillari-Voglauer, R., Fortschegger, K., Gross, S., Gstraunthaler, A., Borth, N., Eisenhaber, F., Lamond, A. I. and Grillari, J. (2011) Exo70, a subunit of the exocyst complex, interacts with SNEV(hPrp19/hPso4) and is involved in pre-mRNA splicing. Biochem J. 438, 81-91
doi. 10.1042/BJ20110183
Pubmed. 21639856

Drakou, C. E., Malekkou, A., Hayes, J. M., Lederer, C. W., Leonidas, D. D., Oikonomakos, N. G., Lamond, A. I., Santama, N. and Zographos, S. E. (2012) hCINAP is an atypical mammalian nuclear adenylate kinase with an ATPase motif: structural and functional studies. Proteins. 80, 206-220
doi. 10.1002/prot.23186
Pubmed. 22038794

Flaus, A. and Owen-Hughes, T. (2011) Mechanisms for ATP-dependent chromatin remodelling: the means to the end. Febs J. 278, 3579-3595
doi. 10.1111/j.1742-4658.2011.08281.x
Pubmed. 21810178

Franz, A., Orth, M., Pirson, P. A., Sonneville, R., Blow, J. J., Gartner, A., Stemmann, O. and Hoppe, T. (2011) CDC-48/p97 coordinates CDT-1 degradation with GINS chromatin dissociation to ensure faithful DNA replication. Mol Cell. 44, 85-96
doi. 10.1016/j.molcel.2011.08.028
Pubmed. 21981920

Gambus, A., Khoudoli, G. A., Jones, R. C. and Blow, J. J. (2011) MCM2-7 form double hexamers at licensed origins in Xenopus egg extract. J Biol Chem. 286, 11855-11864
doi. 10.1074/jbc.M110.199521
Pubmed. 21282109

Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J. L., Barton, G. J. and Owen-Hughes, T. (2011) A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science. 333, 1758-1760
doi. 10.1126/science.1206097
Pubmed. 21940898

Matic, I., Jaffray, E. G., Oxenham, S. K., Groves, M. J., Barratt, C. L., Tauro, S., Stanley-Wall, N. R. and Hay, R. T. (2011) Absolute SILAC-compatible expression strain allows Sumo-2 copy number determination in clinical samples. J Proteome Res. 10, 4869-4875
doi. 10.1021/pr2004715
Pubmed. 21830832

Maure, J. F., Komoto, S., Oku, Y., Mino, A., Pasqualato, S., Natsume, K., Clayton, L., Musacchio, A. and Tanaka, T. U. (2011) The Ndc80 loop region facilitates formation of kinetochore attachment to the dynamic microtubule plus end. Curr Biol. 21, 207-213
doi. 10.1016/j.cub.2010.12.050
Pubmed. 21256019

Mauro, C., Leow, S. C., Anso, E., Rocha, S., Thotakura, A. K., Tornatore, L., Moretti, M., De Smaele, E., Beg, A. A., Tergaonkar, V., Chandel, N. S. and Franzoso, G. (2011) NF-kappaB controls energy homeostasis and metabolic adaptation by upregulating mitochondrial respiration. Nat Cell Biol. 13, 1272-1279
doi. 10.1038/ncb2324
Pubmed. 21968997

Mehrotra, P. V., Ahel, D., Ryan, D. P., Weston, R., Wiechens, N., Kraehenbuehl, R., Owen-Hughes, T. and Ahel, I. (2011) DNA repair factor APLF is a histone chaperone. Mol Cell. 41, 46-55
doi. 10.1016/j.molcel.2010.12.008
Pubmed. 21211722

Melvin, A., Mudie, S. and Rocha, S. (2011) The chromatin remodeler ISWI regulates the cellular response to hypoxia: role of FIH. Mol Biol Cell. 22, 4171-4181
doi. 10.1091/mbc.E11-02-0163
Pubmed. 21900490

Melvin, A., Mudie, S. and Rocha, S. (2011) Further insights into the mechanism of hypoxia-induced NFkappaB. [corrected]. Cell Cycle. 10, 879-882
Pubmed. 21325892

Moore, H. M., Bai, B., Boisvert, F. M., Latonen, L., Rantanen, V., Simpson, J. C., Pepperkok, R., Lamond, A. I. and Laiho, M. (2011) Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation. Mol Cell Proteomics. 10, M111 009241
doi. 10.1074/mcp.M111.009241
Pubmed. 21778410

Moser, S. C. and Swedlow, J. R. (2011) How to be a mitotic chromosome. Chromosome Res. 19, 307-319
doi. 10.1007/s10577-011-9198-3
Pubmed. 21461697

Msaki, A., Sanchez, A. M., Koh, L. F., Barre, B., Rocha, S., Perkins, N. D. and Johnson, R. F. (2011) The role of RelA (p65) threonine 505 phosphorylation in the regulation of cell growth, survival, and migration. Mol Biol Cell. 22, 3032-3040
doi. 10.1091/mbc.E11-04-0280
Pubmed. 21737676

Naidu, S., Friedrich, J. K., Russell, J. and Zomerdijk, J. C. (2011) TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I. Science. 333, 1640-1642
doi. 10.1126/science.1207656
Pubmed. 21921199

Napolitano, L. M., Jaffray, E. G., Hay, R. T. and Meroni, G. (2011) Functional interactions between ubiquitin E2 enzymes and TRIM proteins. Biochem J. 434, 309-319
doi. 10.1042/BJ20101487
Pubmed. 21143188

Nathke, I. and Rocha, S. (2011) Antagonistic crosstalk between APC and HIF-1alpha. Cell Cycle. 10, 1545-1547
Pubmed. 21502812

Ono, M., Scott, M. S., Yamada, K., Avolio, F., Barton, G. J. and Lamond, A. I. (2011) Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res. 39, 3879-3891
doi. 10.1093/nar/gkq1355
Pubmed. 21247878

Plechanovova, A., Jaffray, E. G., McMahon, S. A., Johnson, K. A., Navratilova, I., Naismith, J. H. and Hay, R. T. (2011) Mechanism of ubiquitylation by dimeric RING ligase RNF4. Nat Struct Mol Biol. 18, 1052-1059
doi. 10.1038/nsmb.2108
Pubmed. 21857666

Pourkarimi, E., Greiss, S. and Gartner, A. (2012) Evidence that CED-9/Bcl2 and CED-4/Apaf-1 localization is not consistent with the current model for C. elegans apoptosis induction. Cell Death Differ. 19, 406-415
doi. 10.1038/cdd.2011.104
Pubmed. 21886181

Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K., Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., Berlin, A. M., Desjardins, C. A., Dobbs, E., Dukaj, L., Fan, L., FitzGerald, M. G., French, C., Gujja, S., Hansen, K., Keifenheim, D., Levin, J. Z., Mosher, R. A., Muller, C. A., Pfiffner, J., Priest, M., Russ, C., Smialowska, A., Swoboda, P., Sykes, S. M., Vaughn, M., Vengrova, S., Yoder, R., Zeng, Q., Allshire, R., Baulcombe, D., Birren, B. W., Brown, W., Ekwall, K., Kellis, M., Leatherwood, J., Levin, H., Margalit, H., Martienssen, R., Nieduszynski, C. A., Spatafora, J. W., Friedman, N., Dalgaard, J. Z., Baumann, P., Niki, H., Regev, A. and Nusbaum, C. (2011) Comparative functional genomics of the fission yeasts. Science. 332, 930-936
doi. 10.1126/science.1203357
Pubmed. 21511999

Rutkowski, R., Dickinson, R., Stewart, G., Craig, A., Schimpl, M., Keyse, S. M. and Gartner, A. (2011) Regulation of Caenorhabditis elegans p53/CEP-1-dependent germ cell apoptosis by Ras/MAPK signaling. PLoS Genet. 7, e1002238
doi. 10.1371/journal.pgen.1002238
Pubmed. 21901106

Ryan, D. P. and Owen-Hughes, T. (2011) Snf2-family proteins: chromatin remodellers for any occasion. Curr Opin Chem Biol. 15, 649-656
doi. 10.1016/j.cbpa.2011.07.022
Pubmed. 21862382

Ryan, D. P., Sundaramoorthy, R., Martin, D., Singh, V. and Owen-Hughes, T. (2011) The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. Embo J. 30, 2596-2609
doi. 10.1038/emboj.2011.166
Pubmed. 21623345

Sasaki, T., Li, A., Gillespie, P. J., Blow, J. J. and Gilbert, D. M. (2011) Evidence for a mammalian late-G1 phase inhibitor of replication licensing distinct from geminin or Cdk activity. Nucleus. 2, 455-464
doi. http://dx.doi.org/10.4161/nucl.2.5.1785910.4161/nucl.2.5.17859
Pubmed. 21983086

Scott, M. S., Boisvert, F. M., Lamond, A. I. and Barton, G. J. (2011) PNAC: a protein nucleolar association classifier. BMC Genomics. 12, 74
doi. 10.1186/1471-2164-12-74
Pubmed. 21272300

Swedlow, J. R. (2011) Finding an image in a haystack: the case for public image repositories. Nat Cell Biol. 13, 183
doi. 10.1038/ncb0311-183
Pubmed. 21364564

Swedlow, J. R., Zanetti, G. and Best, C. (2011) Channeling the data deluge. Nat Methods. 8, 463-465
doi. 10.1038/nmeth.1616
Pubmed. 21623351

Tatchell, K., Makrantoni, V., Stark, M. J. and Robinson, L. C. (2011) Temperature-sensitive ipl1-2/Aurora B mutation is suppressed by mutations in TOR complex 1 via the Glc7/PP1 phosphatase. Proc Natl Acad Sci U S A. 108, 3994-3999
doi. 10.1073/pnas.1014406108
Pubmed. 21368139

Tatham, M. H., Matic, I., Mann, M. and Hay, R. T. (2011) Comparative proteomic analysis identifies a role for SUMO in protein quality control. Sci Signal. 4, rs4
doi. 10.1126/scisignal.2001484
Pubmed. 21693764

van Uden, P., Kenneth, N. S., Webster, R., Muller, H. A., Mudie, S. and Rocha, S. (2011) Evolutionary conserved regulation of HIF-1beta by NF-kappaB. PLoS Genet. 7, e1001285
doi. 10.1371/journal.pgen.1001285
Pubmed. 21298084

Vilas-Boas, F., Fior, R., Swedlow, J. R., Storey, K. G. and Henrique, D. (2011) A novel reporter of notch signalling indicates regulated and random Notch activation during vertebrate neurogenesis. BMC Biol. 9, 58
doi. 10.1186/1741-7007-9-58
Pubmed. 21880129

Wang, X. D., Lapi, E., Sullivan, A., Ratnayaka, I., Goldin, R., Hay, R. and Lu, X. (2011) SUMO-modified nuclear cyclin D1 bypasses Ras-induced senescence. Cell Death Differ. 18, 304-314
doi. 10.1038/cdd.2010.101
Pubmed. 20798689

Westman, B. J. and Lamond, A. I. (2011) A role for SUMOylation in snoRNP biogenesis revealed by quantitative proteomics. Nucleus. 2, 30-37
doi. 10.4161/nucl.2.1.14437
Pubmed. 21647297