University of Dundee

Gene Regulation and Expression 2009

Ahel, D., Horejsi, Z., Wiechens, N., Polo, S. E., Garcia-Wilson, E., Ahel, I., Flynn, H., Skehel, M., West, S. C., Jackson, S. P., Owen-Hughes, T. and Boulton, S. J. (2009) Poly(ADP-ribose)-Dependent Regulation of DNA Repair by the Chromatin Remodeling Enzyme ALC1. Science. 325, 1240-1243

Ahmad, Y., Boisvert, F. M., Gregor, P., Cobley, A. and Lamond, A. I. (2009) NOPdb: Nucleolar Proteome Database-2008 update. Nucleic Acids Research. 37, D181-D184

Beckett, M. G., Allton, C. R., Davies, C. T. H., Davis, I., Flynn, J. M., Grant, E. J., Hamilton, R. S., Irving, A. C., Kenway, R. D., Ostrowski, R. H., Perry, J. T., Swedlow, J. R. and Trew, A. (2009) Building a scientific data grid with DIGS. Philosophical Transactions of the Royal Society a-Mathematical Physical and Engineering Sciences. 367, 2471-2481

Bilitou, A., Watson, J., Gartner, A. and Ohnuma, S. I. (2009) The NM23 family in development. Molecular and Cellular Biochemistry. 329, 17-33

Birch, J. L., Tan, B. C. M., Panov, K. I., Panova, T. B., Andersen, J. S., Owen-Hughes, T. A., Russell, J., Lee, S. C. and Zomerdijk, J. (2009) FACT facilitates chromatin transcription by RNA polymerases I and III. Embo Journal. 28, 854-865

Blow, J. J. and Ge, X. Q. (2009) A model for DNA replication showing how dormant origins safeguard against replication fork failure. Embo Reports. 10, 406-412

Cole, C., Sobala, A., Lu, C., Thatcher, S. R., Bowman, A., Brown, J. W. S., Green, P. J., Barton, G. J. and Hutvagner, G. (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. Rna-a Publication of the Rna Society. 15, 2147-2160

De Marco, V., Gillespie, P. J., Li, A., Karantzelis, N., Christodoulou, E., Klompmaker, R., van Gerwen, S., Fish, A., Petoukhov, M. V., Iliou, M. S., Lygerou, Z., Medema, R. H., Blow, J. J., Svergun, D. I., Taraviras, S. and Perrakis, A. (2009) Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing. Proceedings of the National Academy of Sciences of the United States of America. 106, 19807-19812

Engeholm, M., de Jager, M., Flaus, A., Brenk, R., van Noort, J. and Owen-Hughes, T. (2009) Nucleosomes can invade DNA territories occupied by their neighbors. Nature Structural & Molecular Biology. 16, 151-158

Ferrandl, A. I., Storey, K. G. and Swedlow, J. R. (2009) Neurogenesis, mitosis and centrosome: The role of DYRK1A. Mechanisms of Development. 126, S128-S128

Ge, X. Q. and Blow, J. J. (2009) The licensing checkpoint opens up. Cell Cycle. 8, 2320-2322

Geoffroy, M. C. and Hay, R. T. (2009) An additional role for SUMO in ubiquitin-mediated proteolysis. Nature Reviews Molecular Cell Biology. 10, 564-568

Gkikopoulos, T., Havas, K. M., Dewar, H. and Owen-Hughes, T. (2009) SWI/SNF and Asf1p Cooperate To Displace Histones during Induction of the Saccharomyces cerevisiae HO Promoter. Molecular and Cellular Biology. 29, 4057-4066

Golebiowski, F., Matic, I., Tatham, M. H., Cole, C., Yin, Y. L., Nakamura, A., Cox, J., Barton, G. J., Mann, M. and Hay, R. T. (2009) System-Wide Changes to SUMO Modifications in Response to Heat Shock. Science Signaling. 2

Greiss, S. and Gartner, A. (2009) Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Molecules and Cells. 28, 407-415

Grillari, J., Loscher, M., Denegri, M., Lee, K., Fortschegger, K., Eisenhaber, F., Ajuh, P., Lamond, A. I., Katinger, H. and Grillari-Voglauer, R. (2009) Blom7 alpha Is a Novel Heterogeneous Nuclear Ribonucleoprotein K Homology Domain Protein Involved in Pre-mRNA Splicing That Interacts with SNEVPrp19-Pso4. Journal of Biological Chemistry. 284, 29193-29204

Hurd, P. J., Bannister, A. J., Halls, K., Dawson, M. A., Vermeulen, M., Olsen, J. V., Ismail, H., Somers, J., Mann, M., Owen-Hughes, T., Gout, I. and Kouzarides, T. (2009) Phosphorylation of Histone H3 Thr-45 Is Linked to Apoptosis. Journal of Biological Chemistry. 284, 16575-16583

Jablonowski, D., Taubert, J. E., Bar, C., Stark, M. J. R. and Schaffrath, R. (2009) Distinct Subsets of Sit4 Holophosphatases Are Required for Inhibition of Saccharomyces cerevisiae Growth by Rapamycin and Zymocin. Eukaryotic Cell. 8, 1637-1647

Keating, P., Rachidi, N., Tanaka, T. U. and Stark, M. J. R. (2009) Ipl1-dependent phosphorylation of Dam1 is reduced by tension applied on kinetochores. Journal of Cell Science. 122, 4375-4382

Kenneth, N. S., Mudie, S., van Uden, P. and Rocha, S. (2009) SWI/SNF Regulates the Cellular Response to Hypoxia. Journal of Biological Chemistry. 284, 4123-4131

Lake, A., Shield, L. A., Cordano, P., Chui, D. T. Y., Osborne, J., Crae, S., Wilson, K. S., Tosi, S., Knight, S. J. L., Gesk, S., Siebert, R., Hay, R. T. and Jarrett, R. F. (2009) Mutations of NFKBIA, encoding I kappa B alpha, are a recurrent finding in classical Hodgkin lymphoma but are not a unifying feature of non-EBV-associated cases. International Journal of Cancer. 125, 1334-1342

Lamond, A. (2009) Quantitative Analysis of Proteome Localisation and Dynamics. Molecular & Cellular Proteomics, S26-S26

Macaulay, C., Sloan, D., Jiang, X. Y., Forbes, P., Loynton, S., Swedlow, J. R. and Gregor, P. (2009) Usability and User-Centered Design in Scientific Software Development. Ieee Software. 26, 96-102

Makrantoni, V. and Stark, M. J. R. (2009) Efficient Chromosome Biorientation and the Tension Checkpoint in Saccharomyces cerevisiae both Require Bir1. Molecular and Cellular Biology. 29, 4552-4562

Mehlgarten, C., Jablonowski, D., Breunig, K. D., Stark, M. J. R. and Schaffrath, R. (2009) Elongator function depends on antagonistic regulation by casein kinase Hrr25 and protein phosphatase Sit4. Molecular Microbiology. 73, 869-881

Meier, B., Barber, L. J., Liu, Y., Shtessel, L., Boulton, S. J., Gartner, A. and Ahmed, S. (2009) The MRT-1 nuclease is required for DNA crosslink repair and telomerase activity in vivo in Caenorhabditis elegans. Embo Journal. 28, 3549-3563

Moser, S. C., von Elsner, S., Bussing, I., Alpi, A., Schnabel, R. and Gartner, A. (2009) Functional Dissection of Caenorhabditis elegans CLK-2/TEL2 Cell Cycle Defects during Embryogenesis and Germline Development. Plos Genetics. 5

Neumann, H., Hancock, S. M., Buning, R., Routh, A., Chapman, L., Somers, J., Owen-Hughes, T., van Noort, J., Rhodes, D. and Chin, J. W. (2009) A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histories Defines the Effects of H3 K56 Acetylation. Molecular Cell. 36, 153-163

Platani, M., Santarella-Mellwig, R., Posch, M., Walczak, R., Swedlow, J. R. and Mattaj, I. W. (2009) The Nup107-160 Nucleoporin Complex Promotes Mitotic Events via Control of the Localization State of the Chromosome Passenger Complex. Molecular Biology of the Cell. 20, 5260-5275

Scott, M. S., Avolio, F., Ono, M., Lamond, A. I. and Barton, G. J. (2009) Human miRNA Precursors with Box H/ACA snoRNA Features. Plos Computational Biology. 5

Shen, L. N., Geoffroy, M. C., Jaffray, E. G. and Hay, R. T. (2009) Characterization of SENP7, a SUMO-2/3-specific isopeptidase. Biochemical Journal. 421, 223-230

Somers, J. and Owen-Hughes, T. (2009) Mutations to the histone H3 N region selectively alter the outcome of ATP-dependent nucleosome-remodelling reactions. Nucleic Acids Research. 37, 2504-2513

Swedlow, J. R. and Eliceiri, K. W. (2009) Open source bioimage informatics for cell biology. Trends in Cell Biology. 19, 656-660

Swedlow, J. R., Goldberg, I. G., Eliceiri, K. W. and Consortium, O. M. E. (2009) Bioimage Informatics for Experimental Biology. Annual Review of Biophysics. 38, 327-346

Tatham, M. H. and Hay, R. T. (2009) FRET-Based In Vitro Assays for the Analysis of SUMO Protease Activities. Methods in Molecular Biology, 253-268

Tatham, M. H., Rodriguez, M. S., Xirodimas, D. P. and Hay, R. T. (2009) Detection of protein SUMOylation in vivo. Nature Protocols. 4, 1363-1371

von Kriegsheim, A., Baiocchi, D., Birtwistle, M., Sumpton, D., Bienvenut, W., Morrice, N., Yamada, K., Lamond, A., Kalna, G., Orton, R., Gilbert, D. and Kolch, W. (2009) Cell fate decisions are specified by the dynamic ERK interactome. Nature Cell Biology. 11, 1458-U1172