University of Dundee

Gene Regulation and Expression 2010

Awad, S., Ryan, D., Prochasson, P., Owen-Hughes, T. and Hassan, A. H. (2010) The Snf2 Homolog Fun30 Acts as a Homodimeric ATP-dependent Chromatin-remodeling Enzyme. Journal of Biological Chemistry, 285, 9477-9484.

Bailly, A. P., Freeman, A., Hall, J., Declais, A.-C., Alpi, A., Lilley, D. M. J., Ahmed, S. and Gartner, A. (2010) The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair. PLoS Genet, 6, e1001025.

Boisvert, F.-M. and Lamond, A. I. (2010) p53-Dependent subcellular proteome localization following DNA damage. Proteomics, 10, 4087-4097.

Boisvert, F. M., Lam, Y. W., Lamont, D. and Lamond, A. I. (2010) A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage. Molecular & Cellular Proteomics, 9, 457-470.

Boulon, S., Ahmad, Y., Trinkle-Mulcahy, L., Verheggen, C., Cobley, A., Gregor, P., Bertrand, E., Whitehorn, M. and Lamond, A. I. (2010) Establishment of a Protein Frequency Library and Its Application in the Reliable Identification of Specific Protein Interaction Partners. Molecular & Cellular Proteomics, 9, 861-879.

Boulon, S., Pradet-Balade, B., Verheggen, C., Molle, D., Boireau, S., Georgieva, M., Azzag, K., Robert, M. C., Ahmad, Y., Neel, H., Lamond, A. I. and Bertrand, E. (2010) HSP90 and Its R2TP/Prefoldin-like Cochaperone Are Involved in the Cytoplasmic Assembly of RNA Polymerase II. Molecular Cell, 39, 912-924.

Boulon, S., Westman, B. J., Hutten, S., Boisvert, F. M. and Lamond, A. I. (2010) The Nucleolus under Stress. Molecular Cell, 40, 216-227.

Bowman, A., Ward, R., El-Mkami, H., Owen-Hughes, T. and Norman, D. G. (2010) Probing the (H3-H4)(2) histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Research, 38, 695-707.

Castillo-Lluva, S., Tatham, M. H., Jones, R. C., Jaffray, E. G., Edmondson, R. D., Hay, R. T. and Malliri, A. (2010) SUMOylation of the GTPase Rac1 is required for optimal cell migration. Nature Cell Biology, 12, 1078-U1070.

Chadha, G. S. and Blow, J. (2010) Histone Acetylation by HBO1 Tightens Replication Licensing. Molecular Cell, 37, 5-6.

Chamousset, D., De Wever, V., Moorhead, G. B., Chen, Y., Boisvert, F. M., Lamond, A. I. and Trinkle-Mulcahy, L. (2010) RRP1B Targets PP1 to Mammalian Cell Nucleoli and Is Associated with Pre-60S Ribosomal Subunits. Molecular Biology of the Cell, 21, 4212-4226.

Csorba, T., Lozsa, R., Hutvagner, G. and Burgyan, J. (2010) Polerovirus protein P0 prevents the assembly of small RNA-containing RISC complexes and leads to degradation of ARGONAUTE1. Plant Journal, 62, 463-472.

Culver, C., Sundqvist, A., Mudie, S., Melvin, A., Xirodimas, D. and Rocha, S. (2010) Mechanism of Hypoxia-Induced NF-kappa B. Molecular and Cellular Biology, 30, 4901-4921.

Dobbie, I., Kind, E., Parton, R., Carlton, P., Sedat, J. W., Swedlow, J. R. and David, I. (2010) OMX: A new platform for multi-modal, multi-channel widefield imaging. In Live Cell Imaging: A Laboratory Manual, 2nd Edition. (Editors: Spector, D.L., Swedlow, J.R. and Goldman, R.D.). Cold Spring Harbor Laboratory Press, 203-214.

Fox, A. H. and Lamond, A. I. (2010) Paraspeckles. Cold Spring Harbor Perspectives in Biology, 2.

Gallagher, I. J., Scheele, C., Keller, P., Nielsen, A. R., Remenyi, J., Fischer, C. P., Roder, K., Babraj, J., Wahlestedt, C., Hutvagner, G., Pedersen, B. K. and Timmons, J. A. (2010) Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes. Genome Med, 2, 9.

Geoffroy, M. C., Jaffray, E. G., Walker, K. J. and Hay, R. T. (2010) Arsenic-Induced SUMO-Dependent Recruitment of RNF4 into PML Nuclear Bodies. Molecular Biology of the Cell, 21, 4227-4239.

Gillespie, P. J. and Blow, J. J. (2010) Clusters, factories and domains The complex structure of S-phase comes into focus. Cell Cycle, 9, 3218-3226.

Golebiowski, F., Tatham, M. H., Nakamura, A. and Hay, R. T. (2010) High-stringency tandem affinity purification of proteins conjugated to ubiquitin-like moieties. Nature Protocols, 5, 873-882.

Hannoun, Z., Greenhough, S., Jaffray, E., Hay, R. T. and Hay, D. C. (2010) Post-translational modification by SUMO. Toxicology, 278, 288-293.

Hjerpe, R., Aillet, F., Lopitz-Otsoa, F., Lang, V., Torres-Ramos, M., Farras, R., Hay, R. T. and Rodriguez, M. S. (2010) Oligomerization conditions Mdm2-mediated efficient p53 polyubiquitylation but not its proteasomal degradation. International Journal of Biochemistry & Cell Biology, 42, 725-735.

Ito, S., Greiss, S., Gartner, A. and Derry, W. B. (2010) Cell-Nonautonomous Regulation of C. elegans Germ Cell Death by kri-1. Current Biology, 20, 333-338.

Jaqaman, K., King, E. M., Amaro, A. C., Winter, J. R., Dorn, J. F., Elliott, H. L., McHedlishvili, N., McClelland, S. E., Porter, I. M., Posch, M., Toso, A., Danuser, G., McAinsh, A. D., Meraldi, P. and Swedlow, J. R. (2010) Kinetochore alignment within the metaphase plate is regulated by centromere stiffness and microtubule depolymerases. Journal of Cell Biology, 188, 665-679.

Johnston, M., Geoffroy, M. C., Sobala, A., Hay, R. and Hutvagner, G. (2010) HSP90 Protein Stabilizes Unloaded Argonaute Complexes and Microscopic P-bodies in Human Cells. Molecular Biology of the Cell, 21, 1462-1469.

Kenneth, N. S., Mudie, S. and Rocha, S. (2010) IKK and NF-kappa B-mediated regulation of Claspin impacts on ATR checkpoint function. Embo Journal, 29, 2966-2978.

Kitamura, E., Tanaka, K., Komoto, S., Kitamura, Y., Antony, C. and Tanaka, T. U. (2010) Kinetochores Generate Microtubules with Distal Plus Ends: Their Roles and Limited Lifetime in Mitosis. Developmental Cell, 18, 248-259.

Lam, Y. W., Evans, V. C., Heesom, K. J., Lamond, A. I. and Matthews, D. A. (2010) Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells. Molecular & Cellular Proteomics, 9, 117-130.

Lee, S. J., Gartner, A., Hyun, M., Ahn, B. and Koo, H. S. (2010) The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response to DNA Replication Inhibition and Double-Strand DNA Breaks. Plos Genetics, 6.

Li, X., Vadrevu, S., Dunlop, A., Day, J., Advant, N., Troeger, J., Klussmann, E., Jaffrey, E., Hay, R. T., Adams, D. R., Houslay, M. D. and Baillie, G. S. (2010) Selective SUMO modification of cAMP-specific phosphodiesterase-4D5 (PDE4D5) regulates the functional consequences of phosphorylation by PKA and ERK. Biochemical Journal, 428, 55-65.

Linkert, M., Rueden, C. T., Allan, C., Burel, J. M., Moore, W., Patterson, A., Loranger, B., Moore, J., Neves, C., MacDonald, D., Tarkowska, A., Sticco, C., Hill, E., Rossner, M., Eliceiri, K. W. and Swedlow, J. R. (2010) Metadata matters: access to image data in the real world. Journal of Cell Biology, 189, 777-782.

Liu, G. and Xirodimas, D. P. (2010) NUB1 promotes cytoplasmic localization of p53 through cooperation of the NEDD8 and ubiquitin pathways. Oncogene, 29, 2252-2261.

Lleres, D., Denegri, M., Biggiogera, M., Ajuh, P. and Lamond, A. I. (2010) Direct interaction between hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice. EMBO Reports, 11, 445-451.

MacKay, C., Declais, A. C., Lundin, C., Agostinho, A., Deans, A. J., MacArtney, T. J., Hofmann, K., Gartner, A., West, S. C., Helleday, T., Lilley, D. M. J. and Rouse, J. (2010) Identification of KIAA1018/FAN1, a DNA Repair Nuclease Recruited to DNA Damage by Monoubiquitinated FANCD2. Cell, 142, 65-76.

Malekkou, A., Lederer, C. W., Lamond, A. I. and Santama, N. (2010) The nuclear ATPase/adenylate kinase hCINAP is recruited to perinucleolar caps generated upon RNA pol.II inhibition. Febs Letters, 584, 4559-4564.

Monk, C. E., Hutvagner, G. and Arthur, J. S. C. (2010) Regulation of miRNA transcription in macrophages in response to Candida albicans. PLoS One, 5, e13669.

Natsume, T. and Tanaka, T. U. (2010) Spatial regulation and organization of DNA replication within the nucleus. Chromosome Research, 18, 7-17.

Newton, I. P., Kenneth, N. S., Appleton, P. L., Nathke, I. and Rocha, S. (2010) Adenomatous Polyposis Coli and Hypoxia-inducible Factor-1 alpha Have an Antagonistic Connection. Molecular Biology of the Cell, 21, 3630-3638.

Ono, M., Yamada, K., Avolio, F., Scott, M. S., van Koningsbruggen, S., Barton, G. J. and Lamond, A. I. (2010) Analysis of Human Small Nucleolar RNAs (snoRNA) and the Development of snoRNA Modulator of Gene Expression Vectors. Molecular Biology of the Cell, 21, 1569-1584.

Pelisch, F., Gerez, J., Druker, J., Schor, I. E., Munoz, M. J., Risso, G., Petrillo, E., Westman, B. J., Lamond, A. I., Arzt, E. and Srebrow, A. (2010) The serine/arginine-rich protein SF2/ASF regulates protein sumoylation. Proceedings of the National Academy of Sciences of the United States of America, 107, 16119-16124.

Posch, M., Khoudoli, G. A., Swift, S., King, E. M., DeLuca, J. G. and Swedlow, J. R. (2010) Sds22 regulates aurora B activity and microtubule-kinetochore interactions at mitosis. Journal of Cell Biology, 191, 61-74.

Remenyi, J., Hunter, C. J., Cole, C., Ando, H., Impey, S., Monk, C. E., Martin, K. J., Barton, G. J., Hutvagner, G. and Arthur, J. S. C. (2010) Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochemical Journal, 428, 281-291.

Renshaw, M. J., Ward, J. J., Kanemaki, M., Natsume, K., Nedelec, F. J. and Tanaka, T. U. (2010) Condensins Promote Chromosome Recoiling during Early Anaphase to Complete Sister Chromatid Separation. Developmental Cell, 19, 232-244.

Richard, W., Bowman, A., Sozudogru, E., El-Mkami, H., Owen-Hughes, T. and Norman, D. G. (2010) EPR distance measurements in deuterated proteins. Journal of Magnetic Resonance, 207, 164-167.

Rutkowski, R. and Gartner, A. (2010) Tagging the dead: a bridging factor for Caenorhabditis elegans phagocyte receptors. Nature Cell Biology, 12, 638-640.

Rutkowski, R., Hofmann, K. and Gartner, A. (2010) Phylogeny and Function of the Invertebrate p53 Superfamily. Cold Spring Harbor Perspectives in Biology, 2.

Schmitz, M. H. A., Held, M., Janssens, V., Hutchins, J. R. A., Hudecz, O., Ivanova, E., Goris, J., Trinkle-Mulcahy, L., Lamond, A. I., Poser, I., Hyman, A. A., Mechtler, K., Peters, J. M. and Gerlich, D. W. (2010) Live-cell imaging RNAi screen identifies PP2A-B55 alpha and importin-beta 1 as key mitotic exit regulators in human cells. Nature Cell Biology, 12, 886-893.

Scott, M. S., Boisvert, F.-M., McDowall, M. D., Lamond, A. I. and Barton, G. J. (2010) Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res, 38, 7388-7399.

Spector, D. L. and Lamond, A. I. (2010) Nuclear Speckles. Cold Spring Harbor perspectives in biology.

Spector, D. L., Swedlow, J. R. and Goldman, R. D. (2010) Live Cell Imaging: A Laboratory Manual, 2nd Edition. Cold Spring Harbor Laboratory Press.

Stuurman, N. and Swedlow, J. R. (2010) Software tools, data structures and interfaces for microscope imaging.  In Live Cell Imaging: A Laboratory Manual, 2nd Edition. (Editors: Spector, D.L., Swedlow, J.R and Goldman, R.D.). Cold Spring Harbor Laboratory Press, 283-295.

Sun, X. X., Wang, Y. G., Xirodimas, D. P. and Dai, M. S. (2010) Perturbation of 60 S Ribosomal Biogenesis Results in Ribosomal Protein L5-and L11-dependent p53 Activation. Journal of Biological Chemistry, 285, 25812-25821.

Swedlow, J. R. (2010) Advanced hardware and software tools for fast multidimensional imaging of living cells. Proceedings of the National Academy of Sciences of the United States of America, 107, 16005-16006.

Swedlow, J. R., Cotta-Ramusino, C. and Elledge, S. J. (2010) CELL BIOLOGY FORUM Genome-wide view of mitosis. Nature, 464, 684-685.

Swedlow, J. R., Porter, I. M., Posch, M. and Swift, S. (2010) In vivo imaging of mammalian cells. In Live Cell Imaging: A laboratory manual, 2nd Edition (Editors: Spector, D.L., Swedlow, J.R. and Goldman, R.D.). Cold Spring Harbor Laboratory Press, 317-331.

Tanaka, K., Kitamura, E. and Tanaka, T. U. (2010) Live-cell analysis of kinetochore-microtubule interaction in budding yeast. Methods, 51, 206-213.

Tanaka, T. U. (2010) Kinetochore-microtubule interactions: steps towards bi-orientation. The EMBO journal.

Thomson, A. M., Gillespie, P. J. and Blow, J. J. (2010) Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels. Journal of Cell Biology, 188, 209-221.

Uehara, R., Goshima, G., Mabuchi, I., Vale, R. D., Spudich, J. A. and Griffis, E. R. (2010) Determinants of Myosin II Cortical Localization during Cytokinesis. Current Biology, 20, 1080-1085.

van Koningsbruggen, S., Gierlinski, M., Schofield, P., Martin, D., Barton, G. J., Ariyurek, Y., den Dunnen, J. T. and Lamond, A. I. (2010) High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli. Molecular Biology of the Cell, 21, 3735-3748.

Westman, B. J., Verheggen, C., Hutten, S., Lam, Y. W., Bertrand, E. and Lamond, A. I. (2010) A Proteomic Screen for Nucleolar SUMO Targets Shows SUMOylation Modulates the Function of Nop5/Nop58. Molecular Cell, 39, 618-631.

Whitehouse, I. and Owen-Hughes, T. (2010) ATRX: Put Me on Repeat. Cell, 143, 335-336.