University of Dundee

Gene Regulation and Expression 2012

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

Allan, C., Burel, J. M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., Macdonald, D., Moore, W. J., Neves, C., Patterson, A., Porter, M., Tarkowska, A., Loranger, B., Avondo, J., Lagerstedt, I., Lianas, L., Leo, S., Hands, K., Hay, R. T., Patwardhan, A., Best, C., Kleywegt, G. J., Zanetti, G. and Swedlow, J. R. (2012) OMERO: flexible, model-driven data management for experimental biology. Nat Methods. 9, 245-253
doi. 10.1038/nmeth.1896
Pubmed. 22373911

Allan, J., Fraser, R. M., Owen-Hughes, T. and Keszenman-Pereyra, D. (2012) Micrococcal nuclease does not substantially bias nucleosome mapping. J Mol Biol. 417, 152-164
doi. 10.1016/j.jmb.2012.01.043
Pubmed. 22310051

Arabi, A., Ullah, K., Branca, R. M., Johansson, J., Bandarra, D., Haneklaus, M., Fu, J., Aries, I., Nilsson, P., Den Boer, M. L., Pokrovskaja, K., Grander, D., Xiao, G., Rocha, S., Lehtio, J. and Sangfelt, O. (2012) Proteomic screen reveals Fbw7 as a modulator of the NF-kappaB pathway. Nat Commun. 3, 976
doi. 10.1038/ncomms1975
Pubmed. 22864569

Bock, L. J., Pagliuca, C., Kobayashi, N., Grove, R. A., Oku, Y., Shrestha, K., Alfieri, C., Golfieri, C., Oldani, A., Dal Maschio, M., Bermejo, R., Hazbun, T. R., Tanaka, T. U. and De Wulf, P. (2012) Cnn1 inhibits the interactions between the KMN complexes of the yeast kinetochore. Nat Cell Biol. 14, 614-624
doi. 10.1038/ncb2495
Pubmed. 22561345

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. and Owen-Hughes, T. (2012) Sulfyhydryl-reactive site-directed cross-linking as a method for probing the tetrameric structure of histones H3 and H4. Methods Mol Biol. 833, 373-387
doi. 10.1007/978-1-61779-477-3_22
Pubmed. 22183605

Buscaino, A., White, S. A., Houston, D. R., Lejeune, E., Simmer, F., de Lima Alves, F., Diyora, P. T., Urano, T., Bayne, E. H., Rappsilber, J. and Allshire, R. C. (2012) Raf1 Is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification. PLoS Genet. 8, e1002499
doi. 10.1371/journal.pgen.1002499
Pubmed. 22319459

Craig, A. L., Moser, S. C., Bailly, A. P. and Gartner, A. (2012) Methods for studying the DNA damage response in the Caenorhabdatis elegans germ line. Methods Cell Biol. 107, 321-352
doi. 10.1016/B978-0-12-394620-1.00011-4
Pubmed. 22226529

Das, R. M., Wilcock, A. C., Swedlow, J. R. and Storey, K. G. (2012) High-resolution live imaging of cell behavior in the developing neuroepithelium. J Vis Exp
doi. 10.3791/3920
Pubmed. 22525126

Dikovskaya, D., Khoudoli, G., Newton, I. P., Chadha, G. S., Klotz, D., Visvanathan, A., Lamond, A., Swedlow, J. R. and Nathke, I. S. (2012) The adenomatous polyposis coli protein contributes to normal compaction of mitotic chromatin. PLoS One. 7, e38102
doi. 10.1371/journal.pone.0038102
Pubmed. 22719865

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

Engels, B., Jannot, G., Remenyi, J., Simard, M. J. and Hutvagner, G. (2012) Polypyrimidine tract binding protein (hnRNP I) is possibly a conserved modulator of miRNA-mediated gene regulation. PLoS One. 7, e33144
doi. 10.1371/journal.pone.0033144
Pubmed. 22427970

Ganguly, N. (2012) Human papillomavirus-16 E5 protein: oncogenic role and therapeutic value. Cell Oncol (Dordr). 35, 67-76
doi. 10.1007/s13402-011-0069-x
Pubmed. 22262402

Gillespie, P. J., Gambus, A. and Blow, J. J. (2012) Preparation and use of Xenopus egg extracts to study DNA replication and chromatin associated proteins. Methods. 57, 203-213
doi. 10.1016/j.ymeth.2012.03.029
Pubmed. 22521908

Goodfellow, S. J. and Zomerdijk, J. C. (2012) Basic mechanisms in RNA polymerase I transcription of the ribosomal RNA genes. Subcell Biochem. 61, 211-236
doi. 10.1007/978-94-007-4525-4_10
Pubmed. 23150253

Karschau, J., Blow, J. J. and de Moura, A. P. (2012) Optimal placement of origins for DNA replication. Phys Rev Lett. 108, 058101
Pubmed. 22400964

Kisielewska, J. and Blow, J. J. (2012) Dynamic interactions of high Cdt1 and geminin levels regulate S phase in early Xenopus embryos. Development. 139, 63-74
doi. 10.1242/dev.068676
Pubmed. 22096080

Klotz-Noack, K., McIntosh, D., Schurch, N., Pratt, N. and Blow, J. J. (2012) Re-replication induced by geminin depletion occurs from G2 and is enhanced by checkpoint activation. J Cell Sci. 125, 2436-2445
doi. 10.1242/jcs.100883
Pubmed. 22366459

Lamond, A. I., Uhlen, M., Horning, S., Makarov, A., Robinson, C. V., Serrano, L., Hartl, F. U., Baumeister, W., Werenskiold, A. K., Andersen, J. S., Vorm, O., Linial, M., Aebersold, R. and Mann, M. (2012) Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics. 11, O112 017731
doi. 10.1074/mcp.O112.017731
Pubmed. 22311636

Larance, M., Kirkwood, K. J., Xirodimas, D. P., Lundberg, E., Uhlen, M. and Lamond, A. I. (2012) Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway. Mol Cell Proteomics. 11, M111 014407
doi. 10.1074/mcp.M111.014407
Pubmed. 22038470

Leidecker, O. and Xirodimas, D. P. (2012) Isolation of NEDDylated proteins in human cells. Methods Mol Biol. 832, 133-140
doi. 10.1007/978-1-61779-474-2_8
Pubmed. 22350881

Liu, B., Du, H., Rutkowski, R., Gartner, A. and Wang, X. (2012) LAAT-1 is the lysosomal lysine/arginine transporter that maintains amino acid homeostasis. Science. 337, 351-354
doi. 10.1126/science.1220281
Pubmed. 22822152

Mahata, B., Sundqvist, A. and Xirodimas, D. P. (2012) Recruitment of RPL11 at promoter sites of p53-regulated genes upon nucleolar stress through NEDD8 and in an Mdm2-dependent manner. Oncogene. 31, 3060-3071
doi. 10.1038/onc.2011.482
Pubmed. 22081073

Matic, I., Ahel, I. and Hay, R. T. (2012) Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites. Nat Methods. 9, 771-772
doi. 10.1038/nmeth.2106
Pubmed. 22847107

Matic, I. and Hay, R. T. (2012) Detection and quantitation of SUMO chains by mass spectrometry. Methods Mol Biol. 832, 239-247
doi. 10.1007/978-1-61779-474-2_17
Pubmed. 22350890

McIntosh, D. and Blow, J. J. (2012) Dormant origins, the licensing checkpoint, and the response to replicative stresses. Cold Spring Harb Perspect Biol. 4
doi. 10.1101/cshperspect.a012955
Pubmed. 22904560

Melvin, A. and Rocha, S. (2012) Chromatin as an oxygen sensor and active player in the hypoxia response. Cell Signal. 24, 35-43
doi. 10.1016/j.cellsig.2011.08.019
Pubmed. 21924352

Munoz, I. M., MacArtney, T., Sanchez-Pulido, L., Ponting, C. P., Rocha, S. and Rouse, J. (2012) Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator of the SIN3-HDAC1 histone deacetylase complex. J Biol Chem. 287, 32346-32353
doi. 10.1074/jbc.M112.382499
Pubmed. 22865885

Owen-Hughes, T. and Gkikopoulos, T. (2012) Making sense of transcribing chromatin. Curr Opin Cell Biol. 24, 296-304
doi. 10.1016/
Pubmed. 22410403

Plechanovova, A., Jaffray, E. G., Tatham, M. H., Naismith, J. H. and Hay, R. T. (2012) Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature. 489, 115-120
doi. 10.1038/nature11376
Pubmed. 22842904

Pourkarimi, E. and Gartner, A. (2012) If you don't want them shed them. Cell Res
doi. 10.1038/cr.2012.121
Pubmed. 22907666

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

Rutkowski, R. and Gartner, A. (2012) The shark in us: learning about the evolution of the p53 regulatory circuit. Cell Cycle. 11, 216-217
doi. 10.4161/cc.11.2.18901
Pubmed. 22214666

Scott, M. S., Ono, M., Yamada, K., Endo, A., Barton, G. J. and Lamond, A. I. (2012) Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res. 40, 3676-3688
doi. 10.1093/nar/gkr1233
Pubmed. 22199253

Singh, V. and Owen-Hughes, T. (2012) Evolutionary insights into genome-wide nucleosome positioning. Genome Biol. 13, 170
doi. 10.1186/gb4046
Pubmed. 23017016

Sonneville, R., Querenet, M., Craig, A., Gartner, A. and Blow, J. J. (2012) The dynamics of replication licensing in live Caenorhabditis elegans embryos. J Cell Biol. 196, 233-246
doi. 10.1083/jcb.201110080
Pubmed. 22249291

Stuurman, N. and Swedlow, J. R. (2012) Software tools, data structures, and interfaces for microscope imaging. Cold Spring Harb Protoc. 2012, 50-61
doi. 10.1101/pdb.top067504
Pubmed. 22194261

Swedlow, J. and Danuser, G. (2012) Scale integration: the structure and dynamics of macromolecular assemblies, cells and tissues. Curr Opin Cell Biol. 24, 1-3
doi. 10.1016/
Pubmed. 22342264

Swedlow, J. R. (2012) Innovation in biological microscopy: current status and future directions. Bioessays. 34, 333-340
doi. 10.1002/bies.201100168
Pubmed. 22408015

Yin, Y., Seifert, A., Chua, J. S., Maure, J. F., Golebiowski, F. and Hay, R. T. (2012) SUMO-targeted ubiquitin E3 ligase RNF4 is required for the response of human cells to DNA damage. Genes Dev. 26, 1196-1208
doi. 10.1101/gad.189274.112
Pubmed. 22661230

Zhou, W., Hannoun, Z., Jaffray, E., Medine, C. N., Black, J. R., Greenhough, S., Zhu, L., Ross, J. A., Forbes, S., Wilmut, I., Iredale, J. P., Hay, R. T. and Hay, D. C. (2012) SUMOylation of HNF4alpha regulates protein stability and hepatocyte function. J Cell Sci. 125, 3630-3635
doi. 10.1242/jcs.102889
Pubmed. 22505616