University of Dundee

Gene Regulation and Expression 2008

Agostinho, M., Santos, V., Ferreira, F., Costa, R., Cardoso, J., Pinheiro, I., Rino, J., Jaffray, E., Hay, R. T. and Ferreira, J. (2008) Conjugation of human topoisomerase 2 alpha with small ubiquitin-like modifiers 2/3 in response to topoisomerase inhibitors: cell cycle stage and chromosome domain specificity. Cancer research. 68, 2409-2418
doi: 10.1158/0008-5472.CAN-07-2092

Bar, C., Zabel, R., Liu, S., Stark, M. J. and Schaffrath, R. (2008) A versatile partner of eukaryotic protein complexes that is involved in multiple biological processes: Kti11/Dph3. Molecular Microbiology. 69, 1221-1233
doi: 10.1111/j.1365-2958.2008.06350.x

Barton, G. J. (2008) Sequence alignment for molecular replacement. Acta Crystallogr D Biol Crystallogr. 64, 25-32
doi: 10.1107/S0907444907046343
Pubmed: 2394811

Bedford, L., Hay, D., Paine, S., Rezvani, N., Mee, M., Lowe, J. and Mayer, R. J. (2008) Is malfunction of the ubiquitin proteasome system the primary cause of alpha-synucleinopathies and other chronic human neurodegenerative disease? Biochim Biophys Acta. 1782, 683-690
doi: 10.1016/j.bbadis.2008.10.009

Birch, J. L. and Zomerdijk, J. C. (2008) Structure and function of ribosomal RNA gene chromatin. Biochemical Society transactions. 36, 619-624
doi: 10.1042/BST0360619

Blow, J. J. and Ge, X. Q. (2008) Replication forks, chromatin loops and dormant replication origins. Genome biology. 9, 244
doi: 10.1186/gb-2008-9-12-244
Pubmed: 2646269

Blow, J. J. and Gillespie, P. J. (2008) Replication licensing and cancer--a fatal entanglement? Nature reviews. Cancer. 8, 799-806
doi: 10.1038/nrc2500
Pubmed: 2577763

Bru, T., Clarke, C., McGrew, M. J., Sang, H. M., Wilmut, I. and Blow, J. J. (2008) Rapid induction of pluripotency genes after exposure of human somatic cells to mouse ES cell extracts. Experimental cell research. 314, 2634-2642
doi: 10.1016/j.yexcr.2008.05.009
Pubmed: 2577761

Chang, E. Y., Ferreira, H., Somers, J., Nusinow, D. A., Owen-Hughes, T. and Narlikar, G. J. (2008) MacroH2A allows ATP-dependent chromatin remodeling by SWI/SNF and ACF complexes but specifically reduces recruitment of SWI/SNF. Biochemistry. 47, 13726-13732
doi: 10.1021/bi8016944

Cheng, J., Fernando, K. A., Veca, L. M., Sun, Y. P., Lamond, A. I., Lam, Y. W. and Cheng, S. H. (2008) Reversible accumulation of PEGylated single-walled carbon nanotubes in the mammalian nucleus. ACS nano. 2, 2085-2094
doi: 10.1021/nn800461u

Cole, C., Barber, J. D. and Barton, G. J. (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 36, W197-201
doi: 10.1093/nar/gkn238
Pubmed: 2447793

Deutsch, E. W., Ball, C. A., Berman, J. J., Bova, G. S., Brazma, A., Bumgarner, R. E., Campbell, D., Causton, H. C., Christiansen, J. H., Daian, F., Dauga, D., Davidson, D. R., Gimenez, G., Goo, Y. A., Grimmond, S., Henrich, T., Herrmann, B. G., Johnson, M. H., Korb, M., Mills, J. C., Oudes, A. J., Parkinson, H. E., Pascal, L. E., Pollet, N., Quackenbush, J., Ramialison, M., Ringwald, M., Salgado, D., Sansone, S. A., Sherlock, G., Stoeckert, C. J., Jr., Swedlow, J., Taylor, R. C., Walashek, L., Warford, A., Wilkinson, D. G., Zhou, Y., Zon, L. I., Liu, A. Y. and True, L. D. (2008) Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature biotechnology. 26, 305-312
doi: 10.1038/nbt1391

Ellis, J. D., Lleres, D., Denegri, M., Lamond, A. I. and Caceres, J. F. (2008) Spatial mapping of splicing factor complexes involved in exon and intron definition. The Journal of cell biology. 181, 921-934
doi: 10.1083/jcb.200710051
Pubmed: 2426932

Gartner, A., Boag, P. R. and Blackwell, T. K. (2008) Germline survival and apoptosis. WormBook : the online review of C. elegans biology, 1-20
doi: 10.1895/wormbook.1.145.1

Gibson, F., Anderson, L., Babnigg, G., Baker, M., Berth, M., Binz, P. A., Borthwick, A., Cash, P., Day, B. W., Friedman, D. B., Garland, D., Gutstein, H. B., Hoogland, C., Jones, N. A., Khan, A., Klose, J., Lamond, A. I., Lemkin, P. F., Lilley, K. S., Minden, J., Morris, N. J., Paton, N. W., Pisano, M. R., Prime, J. E., Rabilloud, T., Stead, D. A., Taylor, C. F., Voshol, H., Wipat, A. and Jones, A. R. (2008) Guidelines for reporting the use of gel electrophoresis in proteomics. Nature biotechnology. 26, 863-864
doi: 10.1038/nbt0808-863

Gohler, T., Munoz, I. M., Rouse, J. and Blow, J. J. (2008) PTIP/Swift is required for efficient PCNA ubiquitination in response to DNA damage. DNA repair. 7, 775-787
doi: 10.1016/j.dnarep.2008.02.001

Greiss, S., Hall, J., Ahmed, S. and Gartner, A. (2008) C. elegans SIR-2.1 translocation is linked to a proapoptotic pathway parallel to cep-1/p53 during DNA damage-induced apoptosis. Genes & development. 22, 2831-2842
doi: 10.1101/gad.482608
Pubmed: 2569882

Greiss, S., Schumacher, B., Grandien, K., Rothblatt, J. and Gartner, A. (2008) Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family. BMC genomics. 9, 334
doi: 10.1186/1471-2164-9-334
Pubmed: 2491638

Hutvagner, G. and Simard, M. J. (2008) Argonaute proteins: key players in RNA silencing. Nature reviews. Molecular cell biology. 9, 22-32
doi: 10.1038/nrm2321

Jefferson, E. R., Walsh, T. P. and Barton, G. J. (2008) A comparison of SCOP and CATH with respect to domain-domain interactions. Proteins. 70, 54-62
doi: 10.1002/prot.21496

Kenneth, N. S. and Rocha, S. (2008) Regulation of gene expression by hypoxia. The Biochemical journal. 414, 19-29
doi: 10.1042/BJ20081055

Khoudoli, G. A., Gillespie, P. J., Stewart, G., Andersen, J. S., Swedlow, J. R. and Blow, J. J. (2008) Temporal profiling of the chromatin proteome reveals system-wide responses to replication inhibition. Current biology : CB. 18, 838-843
doi: 10.1016/j.cub.2008.04.075
Pubmed: 2440559

Lain, S., Hollick, J. J., Campbell, J., Staples, O. D., Higgins, M., Aoubala, M., McCarthy, A., Appleyard, V., Murray, K. E., Baker, L., Thompson, A., Mathers, J., Holland, S. J., Stark, M. J., Pass, G., Woods, J., Lane, D. P. and Westwood, N. J. (2008) Discovery, in vivo activity, and mechanism of action of a small-molecule p53 activator. Cancer cell. 13, 454-463
doi: 10.1016/j.ccr.2008.03.004
Pubmed: 2742717

Lee, H., Cho, J. S., Lambacher, N., Lee, J., Lee, S. J., Lee, T. H., Gartner, A. and Koo, H. S. (2008) The Caenorhabditis elegans AMP-activated protein kinase AAK-2 is phosphorylated by LKB1 and is required for resistance to oxidative stress and for normal motility and foraging behavior. The Journal of biological chemistry. 283, 14988-14993
doi: 10.1074/jbc.M709115200

Lia, G., Indrieri, M., Owen-Hughes, T., Finzi, L., Podesta, A., Milani, P. and Dunlap, D. (2008) ATP-dependent looping of DNA by ISWI. Journal of biophotonics. 1, 280-286
doi: 10.1002/jbio.200810027

Mangold, U., Hayakawa, H., Coughlin, M., Munger, K. and Zetter, B. R. (2008) Antizyme, a mediator of ubiquitin-independent proteasomal degradation and its inhibitor localize to centrosomes and modulate centriole amplification. Oncogene. 27, 604-613
doi: 10.1038/sj.onc.1210685

Manning, J. R., Jefferson, E. R. and Barton, G. J. (2008) The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC bioinformatics. 9, 51
doi: 10.1186/1471-2105-9-51
Pubmed: 2267696

Martin, S. F., Tatham, M. H., Hay, R. T. and Samuel, I. D. (2008) Quantitative analysis of multi-protein interactions using FRET: application to the SUMO pathway. Protein science : a publication of the Protein Society. 17, 777-784
doi: 10.1110/ps.073369608
Pubmed: 2271167

Matic, I., van Hagen, M., Schimmel, J., Macek, B., Ogg, S. C., Tatham, M. H., Hay, R. T., Lamond, A. I., Mann, M. and Vertegaal, A. C. (2008) In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy. Molecular & cellular proteomics : MCP. 7, 132-144
doi: 10.1074/mcp.M700173-MCP200

Miles, W. O., Jaffray, E., Campbell, S. G., Takeda, S., Bayston, L. J., Basu, S. P., Li, M., Raftery, L. A., Ashe, M. P., Hay, R. T. and Ashe, H. L. (2008) Medea SUMOylation restricts the signaling range of the Dpp morphogen in the Drosophila embryo. Genes & development. 22, 2578-2590
doi: 10.1101/gad.494808
Pubmed: 2546696

Moore, J., Allan, C., Burel, J. M., Loranger, B., MacDonald, D., Monk, J. and Swedlow, J. R. (2008) Open tools for storage and management of quantitative image data. Methods in cell biology. 85, 555-570
doi: 10.1016/S0091-679X(08)85024-8

Moorhead, G. B., Trinkle-Mulcahy, L., Nimick, M., De Wever, V., Campbell, D. G., Gourlay, R., Lam, Y. W. and Lamond, A. I. (2008) Displacement affinity chromatography of protein phosphatase one (PP1) complexes. BMC biochemistry. 9, 28
doi: 10.1186/1471-2091-9-28
Pubmed: 2587467

Mouysset, J., Deichsel, A., Moser, S., Hoege, C., Hyman, A. A., Gartner, A. and Hoppe, T. (2008) Cell cycle progression requires the CDC-48UFD-1/NPL-4 complex for efficient DNA replication. P Natl Acad Sci USA. 105, 12879-12884
doi: 10.1073/pnas.0805944105
Pubmed: 2529102

Mudhasani, R., Zhu, Z., Hutvagner, G., Eischen, C. M., Lyle, S., Hall, L. L., Lawrence, J. B., Imbalzano, A. N. and Jones, S. N. (2008) Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells. The Journal of cell biology. 181, 1055-1063
doi: 10.1083/jcb.200802105
Pubmed: 2442212

Nakai, Y., Nakai, M. and Hayashi, H. (2008) Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems. J Biol Chem. 283, 27469-27476
doi: 10.1074/jbc.M804043200

Overton, I. M., Padovani, G., Girolami, M. A. and Barton, G. J. (2008) ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics. 24, 901-907
doi: 10.1093/bioinformatics/btn055

Overton, I. M., van Niekerk, C. A., Carter, L. G., Dawson, A., Martin, D. M., Cameron, S., McMahon, S. A., White, M. F., Hunter, W. N., Naismith, J. H. and Barton, G. J. (2008) TarO: a target optimisation system for structural biology. Nucleic Acids Research. 36, W190-196
doi: 10.1093/nar/gkn141
Pubmed: 2447720

Richard, D. J., Bolderson, E., Cubeddu, L., Wadsworth, R. I., Savage, K., Sharma, G. G., Nicolette, M. L., Tsvetanov, S., McIlwraith, M. J., Pandita, R. K., Takeda, S., Hay, R. T., Gautier, J., West, S. C., Paull, T. T., Pandita, T. K., White, M. F. and Khanna, K. K. (2008) Single-stranded DNA-binding protein hSSB1 is critical for genomic stability. Nature. 453, 677-681
doi: 10.1038/nature06883

Romao, M., Tanaka, K., Sibarita, J. B., Ly-Hartig, N. T., Tanaka, T. U. and Antony, C. (2008) Three-dimensional electron microscopy analysis of ndc10-1 mutant reveals an aberrant organization of the mitotic spindle and spindle pole body defects in Saccharomyces cerevisiae. Journal of structural biology. 163, 18-28
doi: 10.1016/j.jsb.2008.03.015

Steitz, J. A., Dreyfuss, G., Krainer, A. R., Lamond, A. I., Matera, A. G. and Padgett, R. A. (2008) Where in the cell is the minor spliceosome? P Natl Acad Sci USA. 105, 8485-8486
doi: 10.1073/pnas.0804024105
Pubmed: 2438384

Swedlow, J. R., Rueden, C., Burel, J. M., Linkert, M., Loranger, B., Allan, C. and K.W., E. (2008) Open File Formats for High-Content Analysis. In High Content Screening: Science, Techniques, and Applications. John Wiley and Sons.

Tanaka, T. U. (2008) Bi-orienting chromosomes: acrobatics on the mitotic spindle. Chromosoma. 117, 521-533
doi: 10.1007/s00412-008-0173-5

Tanaka, T. U. and Desai, A. (2008) Kinetochore-microtubule interactions: the means to the end. Current opinion in cell biology. 20, 53-63
doi: 10.1016/
Pubmed: 2358929

Tatham, M. H., Geoffroy, M. C., Shen, L., Plechanovova, A., Hattersley, N., Jaffray, E. G., Palvimo, J. J. and Hay, R. T. (2008) RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation. Nature cell biology. 10, 538-546
doi: 10.1038/ncb1716

Trinkle-Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F. M., Vandermoere, F., Morrice, N. A., Swift, S., Rothbauer, U., Leonhardt, H. and Lamond, A. (2008) Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. The Journal of cell biology. 183, 223-239
doi: 10.1083/jcb.200805092
Pubmed: 2568020

Trinkle-Mulcahy, L. and Lamond, A. I. (2008) Nuclear functions in space and time: gene expression in a dynamic, constrained environment. Febs Letters. 582, 1960-1970
doi: 10.1016/j.febslet.2008.04.029

van Uden, P., Kenneth, N. S. and Rocha, S. (2008) Regulation of hypoxia-inducible factor-1alpha by NF-kappaB. The Biochemical journal. 412, 477-484
doi: 10.1042/BJ20080476
Pubmed: 2474706

Walsh, T. P., Webber, C., Searle, S., Sturrock, S. S. and Barton, G. J. (2008) SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Research. 36, W25-29
doi: 10.1093/nar/gkn320
Pubmed: 2447745

Watson, M. R., Wallace, K., Gieling, R. G., Manas, D. M., Jaffray, E., Hay, R. T., Mann, D. A. and Oakley, F. (2008) NF-kappaB is a critical regulator of the survival of rodent and human hepatic myofibroblasts. Journal of hepatology. 48, 589-597
doi: 10.1016/j.jhep.2007.12.019

Xirodimas, D. P., Sundqvist, A., Nakamura, A., Shen, L., Botting, C. and Hay, R. T. (2008) Ribosomal proteins are targets for the NEDD8 pathway. EMBO Rep. 9, 280-286
doi: 10.1038/embor.2008.10
Pubmed: 2267383

Yamada, Y., Wang, H. Y., Fukuzawa, M., Barton, G. J. and Williams, J. G. (2008) A new family of transcription factors. Development. 135, 3093-3101
doi: 10.1242/dev.026377

Yamamoto, Y., Hoshino, Y., Ito, T., Nariai, T., Mohri, T., Obana, M., Hayata, N., Uozumi, Y., Maeda, M., Fujio, Y. and Azuma, J. (2008) Atrogin-1 ubiquitin ligase is upregulated by doxorubicin via p38-MAP kinase in cardiac myocytes. Cardiovasc Res. 79, 89-96
doi: 10.1093/cvr/cvn076