University of Dundee

Gene Regulation and Expression 2014

Ahmad, Y. and Lamond, A. I. (2014) A perspective on proteomics in cell biology. Trends Cell Biol. 24, 257-264
doi;  10.1016/j.tcb.2013.10.010;
Pubmed; 3989996

Bandarra, D., Biddlestone, J., Mudie, S., Muller, H. A. and Rocha, S. (2014) Hypoxia activates IKK-NF-kappaB and the immune response in Drosophila melanogaster. Bioscience reports. 34
doi;  10.1042/BSR20140095;
Pubmed; 4114064

Bett, J. S., Ibrahim, A. F., Garg, A. K., Rocha, S. and Hay, R. T. (2014) SiRNA screening to identify ubiquitin and ubiquitin-like system regulators of biological pathways in cultured mammalian cells. J Vis Exp
doi;  10.3791/51572;
 
Biddlestone, J., Druker, J., Shmakova, A., Ferguson, G., Swedlow, J. R. and Rocha, S. (2014) Analysis of global RNA synthesis at the single cell level following hypoxia. J Vis Exp
doi;  10.3791/51420;
Pubmed; 4184815

Bizarro, J., Charron, C., Boulon, S., Westman, B., Pradet-Balade, B., Vandermoere, F., Chagot, M. E., Hallais, M., Ahmad, Y., Leonhardt, H., Lamond, A., Manival, X., Branlant, C., Charpentier, B., Verheggen, C. and Bertrand, E. (2014) Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. J Cell Biol. 207, 463-480
doi;  10.1083/jcb.201404160;
Pubmed; 4242836

Bowman, A., Hammond, C. M., Stirling, A., Ward, R., Shang, W., El-Mkami, H., Robinson, D. A., Svergun, D. I., Norman, D. G. and Owen-Hughes, T. (2014) The histone chaperones Vps75 and Nap1 form ring-like, tetrameric structures in solution. Nucleic Acids Res. 42, 6038-6051
doi;  10.1093/nar/gku232;
Pubmed; 4027167

Bremm, A., Moniz, S., Mader, J., Rocha, S. and Komander, D. (2014) Cezanne (OTUD7B) regulates HIF-1alpha homeostasis in a proteasome-independent manner. EMBO Rep. 15, 1268-1277
doi;  10.15252/embr.201438850;
Pubmed; 4264929

Cole, C., Kroboth, K., Schurch, N. J., Sandilands, A., Sherstnev, A., O'Regan, G. M., Watson, R. M., McLean, W. H., Barton, G. J., Irvine, A. D. and Brown, S. J. (2014) Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis. The Journal of allergy and clinical immunology. 134, 82-91
doi;  10.1016/j.jaci.2014.04.021;
Pubmed; 4090750

Cowling, V. H., Turner, S. A. and Cole, M. D. (2014) Burkitt's lymphoma-associated c-Myc mutations converge on a dramatically altered target gene response and implicate Nol5a/Nop56 in oncogenesis. Oncogene. 33, 3519-3527
doi;  10.1038/onc.2013.338;
 
Di Cerbo, V., Mohn, F., Ryan, D. P., Montellier, E., Kacem, S., Tropberger, P., Kallis, E., Holzner, M., Hoerner, L., Feldmann, A., Richter, F. M., Bannister, A. J., Mittler, G., Michaelis, J., Khochbin, S., Feil, R., Schuebeler, D., Owen-Hughes, T., Daujat, S. and Schneider, R. (2014) Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. eLife. 3
doi;  ARTN e01632 DOI 10.7554/eLife.01632;
 
Di Santo, R., Bandau, S. and Stark, M. J. (2014) A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex. Mol Microbiol. 92, 1227-1242
doi;  10.1111/mmi.12624;
Pubmed; 4150532

Dunn, S. and Cowling, V. H. (2014) Myc and mRNA capping. Biochim Biophys Acta
doi;  10.1016/j.bbagrm.2014.03.007;
 
El Mkami, H., Ward, R., Bowman, A., Owen-Hughes, T. and Norman, D. G. (2014) The spatial effect of protein deuteration on nitroxide spin-label relaxation: implications for EPR distance measurement. J Magn Reson. 248, 36-41
doi;  10.1016/j.jmr.2014.09.010;
Pubmed; 4245719

Freeman, A. D., Liu, Y., Declais, A. C., Gartner, A. and Lilley, D. M. (2014) GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes. J Mol Biol. 426, 3946-3959
doi;  10.1016/j.jmb.2014.10.008;
Pubmed; 4270448

Fritah, S., Lhocine, N., Golebiowski, F., Mounier, J., Andrieux, A., Jouvion, G., Hay, R. T., Sansonetti, P. and Dejean, A. (2014) Sumoylation controls host anti-bacterial response to the gut invasive pathogen Shigella flexneri. EMBO Rep. 15, 965-972
doi;  10.15252/embr.201338386;
Pubmed; 4198040

Gonatopoulos-Pournatzis, T. and Cowling, V. H. (2014) Cap-binding complex (CBC). Biochem J. 457, 231-242
doi;  10.1042/BJ20131214;
Pubmed; 3901397

Gonatopoulos-Pournatzis, T. and Cowling, V. H. (2014) RAM function is dependent on Kapbeta2-mediated nuclear entry. Biochem J. 457, 473-484
doi;  10.1042/BJ20131359;
Pubmed; 3898117

Hammond, C. M., Owen-Hughes, T. and Norman, D. G. (2014) Modelling multi-protein complexes using PELDOR distance measurements for rigid body minimisation experiments using XPLOR-NIH. Methods. 70, 139-153
doi;  10.1016/j.ymeth.2014.10.028;
Pubmed; 4274318

Hands, K. J., Cuchet-Lourenco, D., Everett, R. D. and Hay, R. T. (2014) PML isoforms in response to arsenic: high-resolution analysis of PML body structure and degradation. J Cell Sci. 127, 365-375
doi;  10.1242/jcs.132290;
Pubmed; 3889398

Hutten, S., Chachami, G., Winter, U., Melchior, F. and Lamond, A. I. (2014) A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II. J Cell Sci. 127, 1065-1078
doi;  10.1242/jcs.141788;
Pubmed; 3937775

Lang, V., Pallara, C., Zabala, A., Lobato-Gil, S., Lopitz-Otsoa, F., Farras, R., Hjerpe, R., Torres-Ramos, M., Zabaleta, L., Blattner, C., Hay, R. T., Barrio, R., Carracedo, A., Fernandez-Recio, J., Rodriguez, M. S. and Aillet, F. (2014) Tetramerization-defects of p53 result in aberrant ubiquitylation and transcriptional activity. Molecular oncology. 8, 1026-1042
doi;  10.1016/j.molonc.2014.04.002;
 
Lilley, A. C., Major, L., Young, S., Stark, M. J. and Smith, T. K. (2014) The essential roles of cytidine diphosphate-diacylglycerol synthase in bloodstream form Trypanosoma brucei. Mol Microbiol. 92, 453-470
doi;  10.1111/mmi.12553;
Pubmed; 4114554

Ly, T., Ahmad, Y., Shlien, A., Soroka, D., Mills, A., Emanuele, M. J., Stratton, M. R. and Lamond, A. I. (2014) A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. eLife. 3, e01630
doi;  10.7554/eLife.01630;
Pubmed; 3936288

Mackay, C., Carroll, E., Ibrahim, A. F., Garg, A., Inman, G. J., Hay, R. T. and Alpi, A. F. (2014) E3 ubiquitin ligase HOIP attenuates apoptotic cell death induced by cisplatin. Cancer Res. 74, 2246-2257
doi;  10.1158/0008-5472.CAN-13-2131;
Pubmed; 3990471

Makrantoni, V., Corbishley, S. J., Rachidi, N., Morrice, N. A., Robinson, D. A. and Stark, M. J. (2014) Phosphorylation of Sli15 by Ipl1 is important for proper CPC localization and chromosome stability in Saccharomyces cerevisiae. PLoS One. 9, e89399
doi;  10.1371/journal.pone.0089399;
Pubmed; 3928436

Marlow, V. L., Porter, M., Hobley, L., Kiley, T. B., Swedlow, J. R., Davidson, F. A. and Stanley-Wall, N. R. (2014) Phosphorylated DegU Manipulates Cell Fate Differentiation in the Bacillus subtilis Biofilm. Journal of bacteriology. 196, 16-27
doi;  10.1128/jb.00930-13;
 
Masoudi, N., Ibanez-Cruceyra, P., Offenburger, S. L., Holmes, A. and Gartner, A. (2014) Tetraspanin (TSP-17) protects dopaminergic neurons against 6-OHDA-induced neurodegeneration in C. elegans. PLoS Genet. 10, e1004767
doi;  10.1371/journal.pgen.1004767;
Pubmed; 4256090

Meier, B., Cooke, S. L., Weiss, J., Bailly, A. P., Alexandrov, L. B., Marshall, J., Raine, K., Maddison, M., Anderson, E., Stratton, M. R., Gartner, A. and Campbell, P. J. (2014) C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency. Genome research. 24, 1624-1636
doi;  10.1101/gr.175547.114;
Pubmed; 4199376

Meier, B. and Gartner, A. (2014) Having a direct look: Analysis of DNA damage and repair mechanisms by next generation sequencing. Exp Cell Res. 329, 35-41
doi;  DOI 10.1016/j.yexcr.2014.08.011;
 
Moniz, S., Biddlestone, J. and Rocha, S. (2014) Grow(2): the HIF system, energy homeostasis and the cell cycle. Histology and histopathology. 29, 589-600
Mudie, S., Bandarra, D., Batie, M., Biddlestone, J., Moniz, S., Ortmann, B., Shmakova, A. and Rocha, S. (2014) PITX1, a specificity determinant in the HIF-1alpha-mediated transcriptional response to hypoxia. Cell Cycle. 13, 3878-3891
doi;  10.4161/15384101.2014.972889;
 
Olivera-Martinez, I., Schurch, N., Li, R. A., Song, J., Halley, P. A., Das, R. M., Burt, D. W., Barton, G. J. and Storey, K. G. (2014) Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo. Development. 141, 3266-3276
doi;  10.1242/dev.112623;
Pubmed; 4197544

Ortmann, B., Druker, J. and Rocha, S. (2014) Cell cycle progression in response to oxygen levels. Cell Mol Life Sci. 71, 3569-3582
doi;  10.1007/s00018-014-1645-9;
Pubmed; 4143607

Paraskevopoulos, K., Kriegenburg, F., Tatham, M. H., Rosner, H. I., Medina, B., Larsen, I. B., Brandstrup, R., Hardwick, K. G., Hay, R. T., Kragelund, B. B., Hartmann-Petersen, R. and Gordon, C. (2014) Dss1 is a 26S proteasome ubiquitin receptor. Mol Cell. 56, 453-461
doi;  10.1016/j.molcel.2014.09.008;
Pubmed; 4232310

Patwardhan, A., Ashton, A., Brandt, R., Butcher, S., Carzaniga, R., Chiu, W., Collinson, L., Doux, P., Duke, E., Ellisman, M. H., Franken, E., Grunewald, K., Heriche, J. K., Koster, A., Kuhlbrandt, W., Lagerstedt, I., Larabell, C., Lawson, C. L., Saibil, H. R., Sanz-Garcia, E., Subramaniam, S., Verkade, P., Swedlow, J. R. and Kleywegt, G. J. (2014) A 3D cellular context for the macromolecular world. Nat Struct Mol Biol. 21, 841-845
doi;  10.1038/nsmb.2897;
Pubmed; 4346196

Pawellek, A., McElroy, S., Samatov, T., Mitchell, L., Woodland, A., Ryder, U., Gray, D., Luhrmann, R. and Lamond, A. I. (2014) Identification of small molecule inhibitors of pre-mRNA splicing. J Biol Chem. 289, 34683-34698
doi;  10.1074/jbc.M114.590976;
Pubmed; 4263873

Pelisch, F., Sonneville, R., Pourkarimi, E., Agostinho, A., Blow, J. J., Gartner, A. and Hay, R. T. (2014) Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans. Nat Commun. 5, 5485
doi;  10.1038/ncomms6485;
Pubmed; 4268692

Rojas-Fernandez, A., Plechanovova, A., Hattersley, N., Jaffray, E., Tatham, M. H. and Hay, R. T. (2014) SUMO chain-induced dimerization activates RNF4. Mol Cell. 53, 880-892
doi;  10.1016/j.molcel.2014.02.031;
Pubmed; 3991395

Schaffrath, R., Abdel-Fattah, W., Klassen, R. and Stark, M. J. (2014) The diphthamide modification pathway from Saccharomyces cerevisiae--revisited. Mol Microbiol. 94, 1213-1226
doi;  10.1111/mmi.12845;
 
Schurch, N. J., Cole, C., Sherstnev, A., Song, J., Duc, C., Storey, K. G., McLean, W. H., Brown, S. J., Simpson, G. G. and Barton, G. J. (2014) Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PLoS One. 9, e94270
doi;  10.1371/journal.pone.0094270;
Pubmed; 3983147

Shmakova, A., Batie, M., Druker, J. and Rocha, S. (2014) Chromatin and oxygen sensing in the context of JmjC histone demethylases. Biochem J. 462, 385-395
doi;  10.1042/BJ20140754;
Pubmed; 4147966

Speakman, C. M., Domke, T. C., Wongpaiboonwattana, W., Sanders, K., Mudaliar, M., van Aalten, D. M., Barton, G. J. and Stavridis, M. P. (2014) Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ESC differentiation without affecting naive to primed cell transition. Stem cells. 32, 2605-2615
doi;  10.1002/stem.1761;
 
Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F., Tatham, M. H. and Hay, R. T. (2014) Proteome-wide identification of SUMO2 modification sites. Sci Signal. 7, rs2
doi;  10.1126/scisignal.2005146;
Pubmed; 4051997

Trani, D., Nelson, S. A., Moon, B. H., Swedlow, J. J., Williams, E. M., Strawn, S. J., Appleton, P. L., Kallakury, B., Nathke, I. and Fornace, A. J., Jr. (2014) High-energy particle-induced tumorigenesis throughout the gastrointestinal tract. Radiation research. 181, 162-171
doi;  10.1667/RR13502.1;

Tulloch, F., Pathania, U., Luke, G. A., Nicholson, J., Stonehouse, N. J., Rowlands, D. J., Jackson, T., Tuthill, T., Haas, J., Lamond, A. I. and Ryan, M. D. (2014) FMDV replicons encoding green fluorescent protein are replication competent. Journal of virological methods. 209, 35-40
doi;  10.1016/j.jviromet.2014.08.020;
Pubmed; 4201441

Vyas, S., Matic, I., Uchima, L., Rood, J., Zaja, R., Hay, R. T., Ahel, I. and Chang, P. (2014) Family-wide analysis of poly(ADP-ribose) polymerase activity. Nat Commun. 5, 4426
doi;  10.1038/ncomms5426;
Pubmed; 4123609

Xu, Y., Plechanovova, A., Simpson, P., Marchant, J., Leidecker, O., Kraatz, S., Hay, R. T. and Matthews, S. J. (2014) Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4. Nat Commun. 5, 4217
doi;  10.1038/ncomms5217;
Pubmed; 4083429