University of Dundee

Gene Regulation and Expression 2016

Ackermann, L., Schell, M., Pokrzywa, W., Kevei, E., Gartner, A. and Schumacher, B. (2016) E4 ligase-specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis. 23, 995-1002
d.o.i: 10.1038/nsmb.3296
PMC: 27669035
Aregger, M., Kaskar, A., Varshney, D., Fernandez-Sanchez, M. E., Inesta-Vaquera, F. A., Weidlich, S. and Cowling, V. H. (2016) CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription. Molecular cell. 61, 734-746
d.o.i: 10.1016/j.molcel.2016.02.008
PubMed: 4781437
PMC: 26942677
Benatti, P., Belluti, S., Miotto, B., Neusiedler, J., Dolfini, D., Drac, M., Basile, V., Schwob, E., Mantovani, R., Blow, J. J. and Imbriano, C. (2016) Direct non transcriptional role of NF-Y in DNA replication. Biochimica et biophysica acta. 1863, 673-685
d.o.i: 10.1016/j.bbamcr.2015.12.019
PMC: 26732297
Bensaddek, D., Narayan, V., Nicolas, A., Murillo, A. B., Gartner, A., Kenyon, C. J. and Lamond, A. I. (2016) Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics. 16, 381-392
d.o.i: 10.1002/pmic.201500264
PubMed: Pmc4819713
PMC: 26552604
Chadha, G. S., Gambus, A., Gillespie, P. J. and Blow, J. J. (2016) Xenopus Mcm10 is a CDK-substrate required for replication fork stability. Cell cycle (Georgetown, Tex.). 15, 2183-2195
d.o.i: 10.1080/15384101.2016.1199305
PubMed: Pmc4993430
PMC: 27327991
Dickerson, D., Gierlinski, M., Singh, V., Kitamura, E., Ball, G., Tanaka, T. U. and Owen-Hughes, T. (2016) High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. 17, 33
d.o.i: 10.1186/s12860-016-0111-y
PMC: 27609610
D'Ignazio, L. and Rocha, S. (2016) Hypoxia Induced NF-kappaB. Cells. 5
d.o.i: 10.3390/cells5010010
PubMed: 4810095
PMC: 27005664
Esmaeeli-Nieh, S., Fenckova, M., Porter, I. M., Motazacker, M. M., Nijhof, B., Castells-Nobau, A., Asztalos, Z., Weißmann, R., Behjati, F., Tzschach, A., Felbor, U., Scherthan, H., Sayfati, S. M., Ropers, H. H., Kahrizi, K., Najmabadi, H., Swedlow, J. R., Schenck, A. and Kuss, A. W. (2016) BOD1 Is Required for Cognitive Function in Humans and Drosophila. PLoS genetics. 12, e1006022
d.o.i: 10.1371/journal.pgen.1006022
Fennessy, R. T. and Owen-Hughes, T. (2016) Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing. Nucleic Acids Research. 44, 7189-7203
d.o.i: 10.1093/nar/gkw331
PMC: PMC5009725
Froussios, K., Schurch, N. J., Mackinnon, K., Gierlinski, M., Duc, C., Simpson, G. G. and Barton, G. J. (2016) How well do RNA-Seq differential gene expression tools perform in higher eukaryotes? bioRxiv, 090753
Gillespie, P. J., Neusiedler, J., Creavin, K., Chadha, G. S. and Blow, J. J. (2016) Cell Cycle Synchronization in Xenopus Egg Extracts. Methods in molecular biology. 1342, 101-147
d.o.i: 10.1007/978-1-4939-2957-3_6
PMC: 26254920
Grasso, L., Suska, O., Davidson, L., Gonatopoulos-Pournatzis, T., Williamson, R., Wasmus, L., Wiedlich, S., Peggie, M., Stavridis, M. P. and Cowling, V. H. (2016) mRNA Cap Methylation in Pluripotency and Differentiation. Cell reports. 16, 1352-1365
d.o.i: 10.1016/j.celrep.2016.06.089
PubMed: Pmc4977272
PMC: 27452456
Hammond, C. M., Sundaramoorthy, R., Larance, M., Lamond, A., Stevens, M. A., El-Mkami, H., Norman, D. G. and Owen-Hughes, T. (2016) The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3–H4 tetramers and Asf1–H3–H4 complexes. Nucleic Acids Research. 44, 6157-6172
d.o.i: 10.1093/nar/gkw209
Hong, Y., Sonneville, R., Agostinho, A., Meier, B., Wang, B., Blow, J. J. and Gartner, A. (2016) The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis. PLoS genetics. 12, e1005872
d.o.i: 10.1371/journal.pgen.1005872
PubMed: Pmc4807058
PMC: 27010650
Hukelmann, J. L., Anderson, K. E., Sinclair, L. V., Grzes, K. M., Murillo, A. B., Hawkins, P. T., Stephens, L. R., Lamond, A. I. and Cantrell, D. A. (2016) The cytotoxic T cell proteome and its shaping by the kinase mTOR. Nature immunology. 17, 104-112
d.o.i: 10.1038/ni.3314
PubMed: 4685757
PMC: 26551880
Ibrahim-Verbaas, C. A., Bressler, J., Debette, S., Schuur, M., Smith, A. V., Bis, J. C., Davies, G., Trompet, S., Smith, J. A., Wolf, C., Chibnik, L. B., Liu, Y., Vitart, V., Kirin, M., Petrovic, K., Polasek, O., Zgaga, L., Fawns-Ritchie, C., Hoffmann, P., Karjalainen, J., Lahti, J., Llewellyn, D. J., Schmidt, C. O., Mather, K. A., Chouraki, V., Sun, Q., Resnick, S. M., Rose, L. M., Oldmeadow, C., Stewart, M., Smith, B. H., Gudnason, V., Yang, Q., Mirza, S. S., Jukema, J. W., deJager, P. L., Harris, T. B., Liewald, D. C., Amin, N., Coker, L. H., Stegle, O., Lopez, O. L., Schmidt, R., Teumer, A., Ford, I., Karbalai, N., Becker, J. T., Jonsdottir, M. K., Au, R., Fehrmann, R. S., Herms, S., Nalls, M., Zhao, W., Turner, S. T., Yaffe, K., Lohman, K., van Swieten, J. C., Kardia, S. L., Knopman, D. S., Meeks, W. M., Heiss, G., Holliday, E. G., Schofield, P. W., Tanaka, T., Stott, D. J., Wang, J., Ridker, P., Gow, A. J., Pattie, A., Starr, J. M., Hocking, L. J., Armstrong, N. J., McLachlan, S., Shulman, J. M., Pilling, L. C., Eiriksdottir, G., Scott, R. J., Kochan, N. A., Palotie, A., Hsieh, Y. C., Eriksson, J. G., Penman, A., Gottesman, R. F., Oostra, B. A., Yu, L., DeStefano, A. L., Beiser, A., Garcia, M., Rotter, J. I., Nothen, M. M., Hofman, A., Slagboom, P. E., Westendorp, R. G., Buckley, B. M., Wolf, P. A., Uitterlinden, A. G., Psaty, B. M., Grabe, H. J., Bandinelli, S., Chasman, D. I., Grodstein, F., Raikkonen, K., Lambert, J. C., Porteous, D. J., Generation, S., Price, J. F., Sachdev, P. S., Ferrucci, L., Attia, J. R., Rudan, I., Hayward, C., Wright, A. F., Wilson, J. F., Cichon, S., Franke, L., Schmidt, H., Ding, J., de Craen, A. J., Fornage, M., Bennett, D. A., Deary, I. J., Ikram, M. A., Launer, L. J., Fitzpatrick, A. L., Seshadri, S., van Duijn, C. M. and Mosley, T. H. (2016) GWAS for executive function and processing speed suggests involvement of the CADM2 gene. Molecular psychiatry. 21, 189-197
d.o.i: 10.1038/mp.2015.37
PubMed: 4722802
PMC: 25869804
Kapuria, V., Rohrig, U. F., Bhuiyan, T., Borodkin, V. S., van Aalten, D. M., Zoete, V. and Herr, W. (2016) Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes. Genes & development. 30, 960-972
d.o.i: 10.1101/gad.275925.115
PubMed: 4840301
PMC: 27056667
Krupina, K., Kleiss, C., Metzger, T., Fournane, S., Schmucker, S., Hofmann, K., Fischer, B., Paul, N., Porter, I. M., Raffelsberger, W., Poch, O., Swedlow, J. R., Brino, L. and Sumara, I. (2016) Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules. Developmental cell. 36, 63-78
d.o.i: 10.1016/j.devcel.2015.12.017
PMC: 26766443
Lachaud, C., Moreno, A., Marchesi, F., Toth, R., Blow, J. J. and Rouse, J. (2016) Ubiquitinated Fancd2 recruits Fan1 to stalled replication forks to prevent genome instability. Science. 351, 846-849
d.o.i: 10.1126/science.aad5634
PubMed: 4770513
PMC: 26797144
Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. A. and Lamond, A. I. (2016) Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Molecular & cellular proteomics : MCP. 15, 2476-2490
d.o.i: 10.1074/mcp.O115.055467
PubMed: Pmc4937518
PMC: 27114452
Leigh, R., Gault, D., Linkert, M., Burel, J. M., Moore, J., Besson, S. and Swedlow, J. R. (2016) OME Files - An open source reference library for the OME-XML metadata model and the OME-TIFF file format. BioRxiv
d.o.i: 10.1101/087740
Lombardi, O., Varshney, D., Phillips, N. M. and Cowling, V. H. (2016) c-Myc deregulation induces mRNA capping enzyme dependency. Oncotarget. 7, 82273-82288
d.o.i: 10.18632/oncotarget.12701
PMC: 27756891
Maculins, T., Carter, N., Dorval, T., Hudson, K., Nissink, J. W., Hay, R. T. and Alwan, H. (2016) A Generic Platform for Cellular Screening Against Ubiquitin Ligases. Scientific reports. 6, 18940
d.o.i: 10.1038/srep18940
PubMed: 4705515
PMC: 26743172
Maure, J. F., Moser, S. C., Jaffray, E. G., A, F. A. and Hay, R. T. (2016) Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage. Scientific reports. 6, 26178
d.o.i: 10.1038/srep26178
PubMed: 4868978
PMC: 27185577
Moreno, A., Carrington, J. T., Albergante, L., Al Mamun, M., Haagensen, E. J., Komseli, E. S., Gorgoulis, V. G., Newman, T. J. and Blow, J. J. (2016) Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells. Proceedings of the National Academy of Sciences of the United States of America. 113, E5757-5764
d.o.i: 10.1073/pnas.1603252113
PubMed: 5047195
PMC: 27516545
Narayan, V., Ly, T., Pourkarimi, E., Murillo, A. B., Gartner, A., Lamond, A. I. and Kenyon, C. (2016) Deep Proteome Analysis Identifies Age-Related Processes in C. elegans. Cell systems. 3, 144-159
d.o.i: 10.1016/j.cels.2016.06.011
PubMed: 5003814
PMC: 27453442
Ono, M., Yamada, K., Bensaddek, D., Afzal, V., Biddlestone, J., Ortmann, B., Mudie, S., Boivin, V., Scott, M. S., Rocha, S. and Lamond, A. I. (2016) Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1alpha Protein Replacement Human Cell Lines. PloS one. 11, e0154759
d.o.i: 10.1371/journal.pone.0154759
PubMed: 4851398
PMC: 27128805
Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. and Rocha, S. (2016) CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells. Journal of cell science. 129, 191-205
d.o.i: 10.1242/jcs.179911
PubMed: Pmc4732302
PMC: 26644182
Pelisch, F. and Hay, R. T. (2016) Tools to Study SUMO Conjugation in Caenorhabditis elegans. Methods in molecular biology. 1475, 233-256
d.o.i: 10.1007/978-1-4939-6358-4_17
PMC: 27631810 
Raich, L., Borodkin, V., Fang, W., Castro-Lopez, J., van Aalten, D. M., Hurtado-Guerrero, R. and Rovira, C. (2016) A Trapped Covalent Intermediate of a Glycoside Hydrolase on the Pathway to Transglycosylation. Insights from Experiments and Quantum Mechanics/Molecular Mechanics Simulations. Journal of the American Chemical Society. 138, 3325-3332
d.o.i: 10.1021/jacs.5b10092
PMC: 26859322
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. and Barton, G. J. (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA. 22, 839-851
d.o.i: 10.1261/rna.053959.115
PMC: 4878611
Shire, K., Wong, A. I., Tatham, M. H., Anderson, O. F., Ripsman, D., Gulstene, S., Moffat, J., Hay, R. T. and Frappier, L. (2016) Identification of RNF168 as a PML nuclear body regulator. Journal of cell science. 129, 580-591
d.o.i: 10.1242/jcs.176446
PubMed: Pmc4760303
PMC: 26675234
Singh, R., Lawal, H. M., Schilde, C., Gloeckner, G., Barton, G. J., Schaap, P. and Cole, C. (2016) Improved Annotation with de novo Transcripome Assembly in Four Social Amoeba Species. bioRxiv, 054536
Swamy, M., Pathak, S., Grzes, K. M., Damerow, S., Sinclair, L. V. and van Aalten, D. M. (2016) Glucose and glutamine fuel protein O-GlcNAcylation to control T cell self-renewal and malignancy. 17, 712-720
d.o.i: 10.1038/ni.3439
PMC: 27111141
Teresa Pinto, A., Laranjeiro Pinto, M., Patricia Cardoso, A., Monteiro, C., Teixeira Pinto, M., Filipe Maia, A., Castro, P., Figueira, R., Monteiro, A., Marques, M., Mareel, M., Dos Santos, S. G., Seruca, R., Adolfo Barbosa, M., Rocha, S. and Jose Oliveira, M. (2016) Ionizing radiation modulates human macrophages towards a pro-inflammatory phenotype preserving their pro-invasive and pro-angiogenic capacities. Scientific reports. 6, 18765
d.o.i: 10.1038/srep18765
PubMed: 4702523
PMC: 26735768
Trapannone, R., Mariappa, D., Ferenbach, A. T. and van Aalten, D. M. (2016) Nucleocytoplasmic human O-GlcNAc transferase is sufficient for O-GlcNAcylation of mitochondrial proteins. The Biochemical journal. 473, 1693-1702
d.o.i: 10.1042/bcj20160092
PubMed: 4901358
PMC: 27048592
Trapannone, R., Rafie, K. and van Aalten, D. M. (2016) O-GlcNAc transferase inhibitors: current tools and future challenges. Biochemical Society transactions. 44, 88-93
d.o.i: 10.1042/bst20150189
PMC: 26862193
Varshney, D., Petit, A. P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. and Cowling, V. H. (2016) Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic acids research. 44, 10423-10436
d.o.i: 10.1093/nar/gkw637
PubMed: 5137418
PMC: 27422871
Ward, J., Cole, C., Febrer, M. and Barton, G. (2016) AlmostSignificant: Simplifying quality control of high-throughput sequencing data. Bioinformatics
Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. and Owen-Hughes, T. (2016) The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS genetics. 12, e1005940
d.o.i: 10.1371/journal.pgen.1005940
PubMed: 4809547
PMC: 27019336
Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Carazo-Salas, R. E. and Swedlow, J. (2016) The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination. bioRxiv
d.o.i: 10.1101/089359 
Young, D. F., Andrejeva, J., Li, X., Inesta-Vaquera, F., Dong, C., Cowling, V. H., Goodbourn, S. and Randall, R. E. (2016) Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family. Journal of virology. 90, 9446-9456
d.o.i: 10.1128/jvi.01056-16
PubMed: Pmc5044818
PMC: 27512068