University of Dundee

Gene Regulation and Expression 2017

Akay, A., Di Domenico, T., Suen, K. M., Nabih, A., Parada, G. E., Larance, M., Medhi, R., Berkyurek, A. C., Zhang, X., Wedeles, C. J., Rudolph, K. L. M., Engelhardt, J., Hemberg, M., Ma, P., Lamond, A. I., Claycomb, J. M. and Miska, E. A. (2017) The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Developmental cell. 42, 241-255 e246   doi 10.1016/j.devcel.2017.07.002
Pubmed: 28787591   

Alabert, C., Jasencakova, Z. and Groth, A. (2017) Chromatin Replication and Histone Dynamics. Adv Exp Med Biol. 1042, 311-333   doi 10.1007/978-981-10-6955-0_15
Pubmed: 29357065

Alver, R. C., Chadha, G. S., Gillespie, P. J. and Blow, J. J. (2017) Reversal of DDK-Mediated MCM Phosphorylation by Rif1-PP1 Regulates Replication Initiation and Replisome Stability Independently of ATR/Chk1. Cell reports. 18, 2508-2520   doi 10.1016/j.celrep.2017.02.042
Pubmed: 28273463
PMC:5357733

Aregger, M. and Cowling, V. H. (2017) Regulation of mRNA capping in the cell cycle. RNA biology. 14, 11-14   doi 10.1080/15476286.2016.1251540
Pubmed: 27791484
PMC:5270520

Bertolini, S., Wang, B., Meier, B., Hong, Y. and Gartner, A. (2017) Caenorhabditis elegans BUB-3 and SAN-1/MAD3 Spindle Assembly Checkpoint Components Are Required for Genome Stability in Response to Treatment with Ionizing Radiation. G3 (Bethesda). 7, 3875-3885   doi 10.1534/g3.117.1122
Pubmed: 29046436
PMC:5714485

Brenes, A., Afzal, V., Kent, R. and Lamond, A. I. (2018) The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. Nucleic acids research. 46, D1202-D1209   doi 10.1093/nar/gkx807
Pubmed: 28981707
PMC:5753345

Britto-Borges, T. and Barton, G. J. (2017) A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase. PloS one. 12, e0184405   doi 10.1371/journal.pone.0184405
Pubmed: 28886091
PMC:5590929

Chen, Z. H., Singh, R., Cole, C., Lawal, H. M., Schilde, C., Febrer, M., Barton, G. J. and Schaap, P. (2017) Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proceedings of the National Academy of Sciences of the United States of America. 114, 516-521   doi 10.1073/pnas.1608393114
Pubmed: 28057864
PMC:5255622

Crozier, T. W. M., Tinti, M., Larance, M., Lamond, A. I. and Ferguson, M. A. J. (2017) Prediction of Protein Complexes in Trypanosoma brucei by Protein Correlation Profiling Mass Spectrometry and Machine Learning. Molecular & cellular proteomics : MCP. 16, 2254-2267   doi 10.1074/mcp.O117.068122
Pubmed: 29042480
PMC:5724185

Dunn, S., Lombardi, O. and Cowling, V. H. (2017) c-Myc co-ordinates mRNA cap methylation and ribosomal RNA production. The Biochemical journal. 474, 377-384   doi 10.1042/BCJ20160930
Pubmed: 27934633
PMC:5247799

Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. and Lamond, A. I. (2017) The Chromatin Assembly Factor Complex 1 (CAF1) and 5-Azacytidine (5-AzaC) Affect Cell Motility in Src-transformed Human Epithelial Cells. Journal of Biological Chemistry. 292, 172-184   doi 10.1074/jbc.M116.751024
 
Fernandez-Alonso, R., Davidson, L., Hukelmann, J., Zengerle, M., Prescott, A. R., Lamond, A., Ciulli, A., Sapkota, G. P. and Findlay, G. M. (2017) Brd4-Brd2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification. EMBO Rep. 18, 1108-1122   doi 10.15252/embr.201643534
Pubmed: 28588073
PMC:5494510

Flaus, A. and Owen-Hughes, T. (2017) Unlocking the nucleosome. Science. 355, 245-246   doi 10.1126/science.aam5403
Pubmed: 28104852

Froussios, K., Mourao, K., Schurch, N. J. and Barton, G. J. (2017) Identifying differential isoform abundance with RATs: a univeral tool and warning. BioRxiv, 132761
 
Gardner, N. J., Gillespie, P. J., Carrington, J. T., Shanks, E. J., McElroy, S. P., Haagensen, E. J., Frearson, J. A., Woodland, A. and Blow, J. J. (2017) The High-Affinity Interaction between ORC and DNA that Is Required for Replication Licensing Is Inhibited by 2-Arylquinolin-4-Amines. Cell Chem Biol. 24, 981-992 e984   doi 10.1016/j.chembiol.2017.06.019
Pubmed: 28781123
PMC:5563080

Glusman, G., Rose, P. W., Prlic, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T., Karchin, R., Leman, J. K., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. and Deutsch, E. W. (2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 9, 113   doi 10.1186/s13073-017-0509-y
Pubmed: 29254494
PMC:5735928

Gonzalez, A. E., Munoz, V. C., Cavieres, V. A., Bustamante, H. A., Cornejo, V. H., Januario, Y. C., Gonzalez, I., Hetz, C., daSilva, L. L., Rojas-Fernandez, A., Hay, R. T., Mardones, G. A. and Burgos, P. V. (2017) Autophagosomes cooperate in the degradation of intracellular C-terminal fragments of the amyloid precursor protein via the MVB/lysosomal pathway. Faseb J. 31, 2446-2459   doi 10.1096/fj.201600713R
Pubmed: 28254759

Gonzalez-Huici, V., Wang, B. and Gartner, A. (2017) A Role for the Nonsense-Mediated mRNA Decay Pathway in Maintaining Genome Stability in Caenorhabditis elegans. Genetics. 206, 1853-1864   doi 10.1534/genetics.117.203414
Pubmed: 28634159
PMC:5560793

Harvald, E. B., Sprenger, R. R., Dall, K. B., Ejsing, C. S., Nielsen, R., Mandrup, S., Murillo, A. B., Larance, M., Gartner, A., Lamond, A. I. and Faergeman, N. J. (2017) Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans. Cell systems. 5, 38-52 e34   doi 10.1016/j.cels.2017.06.004
Pubmed: 28734827

Hauer, M. H., Seeber, A., Singh, V., Thierry, R., Sack, R., Amitai, A., Kryzhanovska, M., Eglinger, J., Holcman, D., Owen-Hughes, T. and Gasser, S. M. (2017) Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates. Nature structural & molecular biology. 24, 99-107   doi 10.1038/nsmb.3347
Pubmed: 28067915

Hiraga, S. I., Ly, T., Garzon, J., Horejsi, Z., Ohkubo, Y. N., Endo, A., Obuse, C., Boulton, S. J., Lamond, A. I. and Donaldson, A. D. (2017) Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation. EMBO Rep. 18, 403-419   doi 10.15252/embr.201641983
Pubmed: 28077461
PMC:5331243

Hughes, A. L. and Owen-Hughes, T. (2017) Deciphering Subunit-Specific Functions within SWI/SNF Complexes. Cell reports. 18, 2075-2076   doi 10.1016/j.celrep.2017.02.045
Pubmed: 28249153

Inesta-Vaquera, F. and Cowling, V. H. (2017) Regulation and function of CMTR1-dependent mRNA cap methylation. Wiley Interdiscip Rev RNA. 8  doi 10.1002/wrna.1450
Pubmed: 28971629

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., Danecek, P., Faulconbridge, A., Harrison, P. W., Kathuria, A., McCarthy, D., McCarthy, S. A., Meleckyte, R., Memari, Y., Moens, N., Soares, F., Mann, A., Streeter, I., Agu, C. A., Alderton, A., Nelson, R., Harper, S., Patel, M., White, A., Patel, S. R., Clarke, L., Halai, R., Kirton, C. M., Kolb-Kokocinski, A., Beales, P., Birney, E., Danovi, D., Lamond, A. I., Ouwehand, W. H., Vallier, L., Watt, F. M., Durbin, R., Stegle, O. and Gaffney, D. J. (2017) Common genetic variation drives molecular heterogeneity in human iPSCs. Nature  doi 10.1038/nature22403
Pubmed: 28489815

Kumar, A., Tamjar, J., Waddell, A. D., Woodroof, H. I., Raimi, O. G., Shaw, A. M., Peggie, M., Muqit, M. M. and van Aalten, D. M. (2017) Structure of PINK1 and mechanisms of Parkinson's disease-associated mutations. eLife. 6  doi 10.7554/eLife.29985
Pubmed: 28980524
PMC:5679756

Leney, A. C., Rafie, K., van Aalten, D. M. F. and Heck, A. J. R. (2017) Direct Monitoring of Protein O-GlcNAcylation by High-Resolution Native Mass Spectrometry. ACS chemical biology. 12, 2078-2084   doi 10.1021/acschembio.7b00371
Pubmed: 28609614
PMC:5565903

Li, S., Yue, Z. and Tanaka, T. U. (2017) Smc3 Deacetylation by Hos1 Facilitates Efficient Dissolution of Sister Chromatid Cohesion during Early Anaphase. Molecular cell. 68, 605-614 e604   doi 10.1016/j.molcel.2017.10.009
Pubmed: 29100057
PMC:5678280

Logie, L., Van Aalten, L., Knebel, A., Force, T., Hastie, C. J., MacLauchlan, H., Campbell, D. G., Gourlay, R., Prescott, A., Davidson, J., Fuller, W. and Sutherland, C. (2017) Rab-GTPase binding effector protein 2 (RABEP2) is a primed substrate for Glycogen Synthase kinase-3 (GSK3). Scientific reports. 7, 17682   doi 10.1038/s41598-017-17087-6
Pubmed: 29247183
PMC:5732219

Ly, T. and Lamond, A. I. (2017) New Apex in Proteome Analysis. Cell systems. 4, 581-582   doi 10.1016/j.cels.2017.06.009
Pubmed: 28662382

Ly, T., Whigham, A., Clarke, R., Brenes-Murillo, A. J., Estes, B., Madhessian, D., Lundberg, E., Wadsworth, P. and Lamond, A. I. (2017) Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS. eLife. 6  doi 10.7554/eLife.27574
Pubmed: 29052541
PMC:5650473
Makrantoni, V., Ciesiolka, A., Lawless, C., Fernius, J., Marston, A., Lydall, D. and Stark, M. J. R. (2017) A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis. G3 (Bethesda). 7, 3203-3215   doi 10.1534/g3.117.300089
Pubmed: 28754723
PMC5592945

Maric, M., Mukherjee, P., Tatham, M. H., Hay, R. and Labib, K. (2017) Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication. Cell reports. 18, 3033-3042   doi 10.1016/j.celrep.2017.03.020
Pubmed: 28355556
PMC:5382235

Mehlgarten, C., Prochaska, H., Hammermeister, A., Abdel-Fattah, W., Wagner, M., Krutyholowa, R., Jun, S. E., Kim, G. T., Glatt, S., Breunig, K. D., Stark, M. J. R. and Schaffrath, R. (2017) Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator. Toxins (Basel). 9  doi 10.3390/toxins9090272
Pubmed: 28872616
PMC:5618205

Mishra, A., Oules, B., Pisco, A. O., Ly, T., Liakath-Ali, K., Walko, G., Viswanathan, P., Tihy, M., Nijjher, J., Dunn, S. J., Lamond, A. I. and Watt, F. M. (2017) A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis. eLife. 6  doi 10.7554/eLife.27356
Pubmed: 29043977
PMC:5667932

Offenburger, S. L., Bensaddek, D., Murillo, A. B., Lamond, A. I. and Gartner, A. (2017) Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development. Scientific reports. 7, 4314   doi 10.1038/s41598-017-04375-4
Pubmed: 28659600
PMC:5489525

Patwardhan, A., Carazo, J. M., Carragher, B., Henderson, R., Heymann, J. B., Hill, E., Jensen, G. J., Lagerstedt, I., Lawson, C. L., Ludtke, S. J., Mastronarde, D., Moore, W. J., Roseman, A., Rosenthal, P., Sorzano, C. O., Sanz-Garcia, E., Scheres, S. H., Subramaniam, S., Westbrook, J., Winn, M., Swedlow, J. R. and Kleywegt, G. J. (2012) Data management challenges in three-dimensional EM. Nature structural & molecular biology. 19, 1203-1207   doi 10.1038/nsmb.2426
Pubmed: 23211764

Pelisch, F., Tammsalu, T., Wang, B., Jaffray, E. G., Gartner, A. and Hay, R. T. (2017) A SUMO-Dependent Protein Network Regulates Chromosome Congression during Oocyte Meiosis. Molecular cell. 65, 66-77   doi 10.1016/j.molcel.2016.11.001
Pubmed: 27939944
PMC:5222697

Rafie, K., Raimi, O., Ferenbach, A. T., Borodkin, V. S., Kapuria, V. and van Aalten, D. M. F. (2017) Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats. Open biology. 7  doi 10.1098/rsob.170078
Pubmed: 28659383
PMC:5493779

Schleicher, K., Porter, M., Ten Have, S., Sundaramoorthy, R., Porter, I. M. and Swedlow, J. R. (2017) The Ndc80 complex targets Bod1 to human mitotic kinetochores. Open biology. 7  doi 10.1098/rsob.170099
Pubmed: 29142109
PMC:5717335

Selvan, N., Williamson, R., Mariappa, D., Campbell, D. G., Gourlay, R., Ferenbach, A. T., Aristotelous, T., Hopkins-Navratilova, I., Trost, M. and van Aalten, D. M. F. (2017) A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nature chemical biology  doi 10.1038/nchembio.2404
Pubmed: 28604694

Selvan, N., Williamson, R., Mariappa, D., Campbell, D. G., Gourlay, R., Ferenbach, A. T., Aristotelous, T., Hopkins-Navratilova, I., Trost, M. and van Aalten, D. M. F. (2017) A mutant O-GlcNAcase enriches Drosophila developmental regulators. Nature chemical biology. 13, 882-887   doi 10.1038/nchembio.2404
Pubmed: 28604694

Singh, R., Lawal, H. M., Schilde, C., Glockner, G., Barton, G. J., Schaap, P. and Cole, C. (2017) Improved annotation with de novo transcriptome assembly in four social amoeba species. BMC Genomics. 18, 120   doi 10.1186/s12864-017-3505-0
Pubmed: 28143409
PMC:5282741

Sonneville, R., Moreno, S. P., Knebel, A., Johnson, C., Hastie, C. J., Gartner, A., Gambus, A. and Labib, K. (2017) CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Nature cell biology. 19, 468-479   doi 10.1038/ncb3500
Pubmed: 28368371
PMC:5410169

Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Bottcher, B., Norman, D. G. and Owen-Hughes, T. (2017) Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife. 6  doi 10.7554/eLife.22510
Pubmed: 28332978
PMC:5391205

Tatham, M. H., Cole, C., Scullion, P., Wilkie, R., Westwood, N. J., Stark, L. A. and Hay, R. T. (2017) A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome. Molecular & cellular proteomics : MCP. 16, 310-326   doi 10.1074/mcp.O116.065219
Pubmed: 27913581
PMC:5294217

Vasileva, V., Gierlinski, M., Yue, Z., O'Reilly, N., Kitamura, E. and Tanaka, T. U. (2017) Molecular mechanisms facilitating the initial kinetochore encounter with spindle microtubules. J Cell Biol. 216, 1609-1622   doi 10.1083/jcb.201608122
Pubmed: 28446512

Willems, A. P., Gundogdu, M., Kempers, M. J. E., Giltay, J. C., Pfundt, R., Elferink, M., Loza, B. F., Fuijkschot, J., Ferenbach, A. T., van Gassen, K. L. I., van Aalten, D. M. F. and Lefeber, D. J. (2017) Mutations in N-acetylglucosamine (O-GlcNAc) transferase in patients with X-linked intellectual disability. J Biol Chem. 292, 12621-12631   doi 10.1074/jbc.M117.790097
Pubmed: 28584052
PMC:5535036

Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Salas, R. E. C. and Swedlow, J. R. (2017) The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods. 14, 775-781   doi 10.1038/nmeth.4326
Pubmed: 28775673
PMC:5536224

Yue, Z., Komoto, S., Gierlinski, M., Pasquali, D., Kitamura, E. and Tanaka, T. U. (2017) Mechanisms mitigating problems with multiple kinetochores on one microtubule in early mitosis. Journal of cell science  doi 10.1242/jcs.203000
Pubmed: 28546446