University of Dundee

Gene Regulation and Expression 2018

Alabert C, Jasencakova Z, Groth A. 2018. Chromatin Replication and Histone Dynamics. Masai H, Foiani M, editors.  In DNA Replication : From Old Principals to New Discoveries. Singapore: Springer Nature. Pp. 311-333. (Advances in Experimental Medicine and Biology) 10.1007/978-981-10-6955-0_15

Barini E, Miccoli A, Tinarelli F, Mulholland K, Kadri H, Khanim F, Stojanovski L, Read KD, Burness K, Blow JJ, Mehellou Y, Muqit MMK. 2018. The Anthelmintic Drug Niclosamide and Its Analogues Activate the Parkinson's Disease Associated Protein Kinase PINK1. ChemBioChem. 19(5):425-429. https://doi.org/10.1002/cbic.201700500

Bensaddek D, Nicolas A, Lamond AI. 2019. Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes. Current Opinion in Chemical Biology. 48:114-122. https://doi.org/10.1016/j.cbpa.2018.10.011

Borodkin VS, Rafie K, Selvan N, Aristotelous T, Navratilova I, Ferenbach AT, Van Aalten DMF. 2018. O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry. ACS Chemical Biology. 13(5):1353-1360. https://doi.org/10.1021/acschembio.8b00183

Brenes Murillo A, Afzal V, Kent R, Lamond A. 2018. The Encyclopedia of Proteome Dynamics – A big data ecosystem for (prote)omics. Nucleic Acids Research. 46(D1):D1202-D1209. https://doi.org/10.1093/nar/gkx807

Brenes Murillo A, Lamond A. 2018. The Encyclopedia of Proteome Dynamics: The KinoViewer. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty823

Bustos F, Segarra Fas A, Chaugule VK, Brandenburg L, Branigan E, Toth R, Macartney T, Knebel A, Hay R, Walden H, Findlay G. 2018. RNF12 X-linked intellectual disability mutations disrupt E3 ligase activity and neural differentiation. Cell Reports. 23:1599-1611. https://doi.org/10.1016/j.celrep.2018.04.022

Carroll T, Newton I, Chen Y, Blow J, Nathke I. 2018. Lgr5+ intestinal stem cells reside in an unlicensed G1 phase. Journal of Cell Biology. 217(5):1667-1685. https://doi.org/10.1083/jcb.201708023

Crozier TWM, Tinti M, Wheeler RJ, Ly T, Ferguson MAJ, Lamond AI. 2018. Proteomic analysis of the cell cycle of procylic form Trypanosoma brucei. Molecular & Cellular Proteomics. 17:1184-1195. https://doi.org/10.1074/mcp.RA118.000650

Delso I, Valero-Gonzalez J, Gomollón-Bel F, Castro-López J, Fang W, Navratilova I, van Aalten DMF, Tejero T, Merino P, Hurtado-Guerrero R. 2018. Inhibitors against Fungal Cell Wall Remodeling Enzymes. ChemMedChem. 13(2):128-132. https://doi.org/10.1002/cmdc.201700720

Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E. 2018. A call for public archives for biological image data. Nature Methods. 15(11):849-854. https://doi.org/10.1038/s41592-018-0195-8

Gali VK, Dickerson D, Katou Y, Fujiki K, Shirahige K, Owen-Hughes T, Kubota T, Donaldson AD. 2018. Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation. PLoS Genetics. 14(11):e1007783. https://doi.org/10.1371/journal.pgen.1007783

Galloway A, Cowling V. 2018. mRNA cap regulation in mammalian cell function and fate. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. https://doi.org/10.1016/j.bbagrm.2018.09.011

Ghirardello M, Perrone D, Chinaglia N, Sádaba D, Delso I, Tejero T, Marchesi E, Fogagnolo M, Rafie K, van Aalten DMF, Merino P. 2018. UDP-GlcNAc Analogues as Inhibitors of O-GlcNAc Transferase (OGT): Spectroscopic, Computational, and Biological Studies. Chemistry: a European Journal. 24(28):7264-7272. https://doi.org/10.1002/chem.201801083

Gray KM, Kaifer KA, Baillat D, Wen Y, Bonacci TR, Ebert AD, Raimer AC, Spring AM, Have ST, Glascock JJ, Gupta K, Van Duyne GD, Emanuele MJ, Lamond AI, Wagner EJ, Lorson CL, Matera AG. 2018. Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCFSlmb degron. Molecular Biology of the Cell. 29(2):96-110. https://doi.org/10.1091/mbc.E17-11-0627

Gundogdu M, Llabres S, Gorelik A, Ferenbach A, Zachariae U, Van Aalten D. 2018. The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix. Cell Chemical Biology. 25:1-6. https://doi.org/10.1016/j.chembiol.2018.03.004

Hong Y, Sonneville R, Wang B, Scheidt V, Meier B, Woglar A, Demetriou S, Labib K, Jantsch V, Gartner A. 2018. LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis. Nature Communications. 9:1-11. https://doi.org/10.1038/s41467-018-03135-w

Hong Y, Velkova M, Silva N, Jagut M, Scheidt V, Labib K, Jantsch V, Gartner A. 2018. The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans. PLoS Genetics. 14(6):1-22. https://doi.org/10.1371/journal.pgen.1007453

Inesta-Vaquera F, Chaugule VK, Galloway A, Chandler L, Rojas-Fernandez A, Weidlich S, Peggie M, Cowling V. 2018. DHX15 regulates CMTR1-dependent gene expression and cell proliferation. Life Science Alliance. 1(3). https://doi.org/10.26508/lsa.201800092

Jantsch M, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant J-Y, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R. 2018. Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA Biology. 15(6):829-831. https://doi.org/10.1080/15476286.2018.1460996

Jonik-Nowak B, Menneteau T, Fesquet D, Baldin V, Bonne-Andrea C, Méchali F, Fabre B, Boisguerin P, de Rossi S, Henriquet C, Pugnière M, Ducoux-Petit M, Burlet-Schiltz O, Lamond A, Fort P, Boulon S, Bousquet M-P, Coux O. 2018. PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ. Proceedings of the National Academy of Sciences of the United States of America. 115(28):E6477-E6486. https://doi.org/10.1073/pnas.1722299115

Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W. 2018. The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT: UDP-GlcNAc glycosylation and proteolysis activities. Journal of Biological Chemistry. 293(46):17754-17768. https://doi.org/10.1074/jbc.RA118.004185

Kelner A, Tinti M, Guther M, Foth BJ, Chappell L, Berriman M, Cowling V, Ferguson M. 2018. The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei. PLoS ONE. 13(7). https://doi.org/10.1371/journal.pone.0201263

Liakath-Ali K, Mills EW, Sequeira I, Lichtenberger BM, Pisco AO, Sipilä KH, Mishra A, Yoshikawa H, Wu CC-C, Ly T, Lamond AI, Adham IM, Green R, Watt FM. 2018. An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis. Nature. 556:376-380. https://doi.org/10.1038/s41586-018-0032-3

Liu Y, Freeman A, Déclais A-C, Gartner A, Lilley DMJ. 2018. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Spies M, Malkova A, editors. In Mechanisms of DNA Recombination and Genome Rearrangements: Methods to Study Homologous Recombination. Academic Press. pp. 543-568. (Methods in Enzymology). https://doi.org/10.1016/bs.mie.2017.11.021

Loftus RM, Assmann N, Kedia-Mehta N, O'Brien KL, Garcia A, Gillespie C, Hukelmann JL, Oefner PJ, Lamond AI, Gardiner CM, Dettmer K, Cantrell DA, Sinclair LV, Finlay DK. 2018. Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice. Nature Communications. 9(1):1-15. https://doi.org/10.1038/s41467-018-04719-2

Ly T, Endo A, Brenes A, Gierlinski M, Afzal V, Pawellek A, Lamond AI. 2018. Proteome-wide analysis of protein abundance and turnover remodelling during oncogenic transformation of human breast epithelial cells. Wellcome Open Research. 3:1-48. https://doi.org/10.12688/wellcomeopenres.14392.1

Mariappa DN, Ferenbach A, van Aalten DMF. 2018. Effects of hypo O-GlcNAcylation on Drosophila development. Journal of Biological Chemistry. 293(19):7209-7221. https://doi.org/10.1074/jbc.RA118.002580

Matera AG, Raimer AC, Schmidt CA, Kelly JA, Droby GN, Baillat D, Ten Have S, Lamond AI, Wagner EJ, Gray KM. 2018. Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster. G3 : Genes, Genomes, Genetics. 8(12).

Meier B, Volkova NV, Hong Y, Schofield P, Campbell PJ, Gerstung M, Gartner A. 2018. Mutational signatures of DNA mismatch repair deficiency in and human cancers. Genome Research. 28(5):666-675. https://doi.org/10.1101/gr.226845.117

Münceberg S, Hay RT, Ip WH, Meyer T, Weiß C, Brenke J, Masser S, Hadian K, Dobner T, Schreiner S. 2018. E1B-55K mediated regulation of RNF4 STUbL promotes HAdV gene expression. Journal of Virology. 92(13). https://doi.org/10.1128/JVI.00164-18

O'Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore W, Stenau E, Swedlow J, Vuong J, Procter J. 2018. Visualization of Biomedical Data. Annual Review of Biomedical Data Science. 1. https://doi.org/10.1146/annurev-biodatasci-080917-013424

Offenburger S-L, Jongsma E, Gartner A. 2018. Mutations in Caenorhabditis elegans neuroligin-like glit-1, the apoptosis pathway and the calcium chaperone crt-1 increase dopaminergic neurodegeneration after 6-OHDA treatment. PLoS Genetics. 14(1):1-34. https://doi.org/10.1371/journal.pgen.1007106

Offenburger S-L, Ho XY, Tachie-Menson T, Coakley S, Hilliard MA, Gartner A. 2018. 6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33. PLoS Genetics. 14(1):1-27. https://doi.org/10.1371/journal.pgen.1007125

Offenburger S-L, Gartner A. 2018. 6-hydroxydopamine (6-OHDA) Oxidative Stress Assay for Observing Dopaminergic Neuron Loss in Caenorhabditis elegans. Bio-Protocol. 8(18). https://doi.org/10.21769/BioProtoc.3025

Ostrowski A, Cianfanelli FR, Porter M, Mariano G, Peltier J, Wong JJ, Swedlow JR, Trost M, Coulthurst SJ. 2018. Killing with proficiency: integrated post-translational regulation of an offensive Type VI secretion system. PLoS Pathogens. 14(7). https://doi.org/10.1371/journal.ppat.1007230

Pao K-C, Wood NT, Knebel A, Rafie K, Stanley M, Mabbitt PD, Sundaramoorthy R, Hofmann K, van Aalten DMF, Virdee S. 2018. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Nature. 556(7701):381-385. https://doi.org/10.1038/s41586-018-0026-1

Rafie K, Gorelik A, Trapannone R, Borodkin V, Van Aalten D. 2018. Thio-linked UDP-peptide conjugates as O-GlcNAc transferase inhibitors. Bioconjugate Chemistry. 3/5/18. https://doi.org/10.1021/acs.bioconjchem.8b00194

Raimi OG, Hurtado Guerrero R, van Aalten DMF. 2018. Evidence for substrate assisted catalysis in N-acetylphosphoglucosamine mutase. The Biochemical journal. 475(15):2547-2557. https://doi.org/10.1042/BCJ20180172

Schenstrøm SM, Rebula CA, Tatham MH, Hendus-Altenburger R, Jourdain I, Hay RT, Kragelund BB, Hartmann-Petersen R. 2018. Expanded Interactome of the Intrinsically Disordered Protein Dss1. Cell Reports. 25(4):862-870. https://doi.org/10.1016/j.celrep.2018.09.080

Shoaib M, Walter D, Gillespie PJ, Izard F, Fahrenkrog B, Lleres D, Lerdrup M, Johansen JV, Hansen K, Julien E, Blow JJ, Sørensen CS. 2018. Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing. Nature Communications. 9(1). https://doi.org/10.1038/s41467-018-06066-8

Sundaramoorthy R, Hughes A, El-Mkami H, Norman D, Owen-Hughes T. 2018. Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. eLife. 2018(7). https://doi.org/10.7554/eLife.35720

Varshney D, Lombardi O, Schweikert G, Dunn S, Suska O, Cowling V. 2018. mRNA cap methyltransferase, RNMT-RAM, promotes RNA pol II-dependent transcription. Cell Reports. 23(5):1530-1542. https://doi.org/10.1016/j.celrep.2018.04.004

Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR. 2018. Publisher Correction: Image Data Resource: a bioimage data integration and publication platform. Nature Methods. https://doi.org/10.1038/s41592-018-0169-x

Yoshikawa H, Larance M, Ly T, Lamond A. 2018. Efficient Analysis of Mammalian Polysomes in cells and tissues using Ribo Mega-SEC. eLife. 7(7). https://doi.org/10.7554/eLife.36530

Zdankowski P, Trusiak M, Cywinska M, Swedlow JR. 2018. An adaptive optics 3D STED microscope for super-resolution imaging of thick samples with background noise suppression using digital image processing. Jaroszewicz LR, Kujawinska M, editors. In Speckle 2018: VII International Conference on Speckle Metrology. SPIE-International Society for Optical Engineering. https://doi.org/10.1117/12.2324145