Gene Regulation and Expression

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2020

A mechanism-inspired UDP-N-acetylglucosamine pyrophosphorylase inhibitor

Raimi, O., Hurtado-Guerrero, R., Borodkin, V., Ferenbach, A., Urbaniak, M., Ferguson, M. & van Aalten, D., 1 Apr 2020, In : RSC Chemical Biology. 1, p. 13-25 13 p.

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An intellectual disability syndrome with single nucleotide variants in O-GlcNAc Transferase

Pravata, V., Omelkova, M., Stavridis, M., Desbiens, C. M., Stephen, H. M., Lefeber, D. J., Gécz, J., Gundogdu, M., Õunap, K., Joss, S., Schwartz, C. E., Wells, L. & van Aalten, D., 1 Jun 2020, In : European Journal of Human Genetics. 28, p. 706-714 9 p.

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Antibody RING-Mediated Destruction of Endogenous Proteins

Ibrahim, A. F. M., Shen, L., Tatham, M. H., Dickerson, D., Prescott, A. R., Abidi, N., Xirodimas, D. P. & Hay, R. T., 25 May 2020, In : Molecular Cell. 12 p.

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CAP-MAP: cap analysis protocol with minimal analyte processing, a rapid and sensitive approach to analysing mRNA cap structures

Galloway, A., Atrih, A., Grzela, R., Darzynkiewicz, E., Ferguson, M. A. J. & Cowling, V. H., 26 Feb 2020, In : Open Biology. 10, 2, p. 1-13 13 p., 190306.

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Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

McCarthy, D. J., Rostom, R., Huang, Y., Kunz, D. J., Danecek, P., Bonder, M. J., Hagai, T., Lyu, R., Wang, W., Gaffney, D. J., Simons, B. D., Stegle, O. & Teichmann, S. A., 16 Mar 2020, In : Nature Methods. 17, 4, p. 414-421 8 p.

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Cyclin A triggers Mitosis either via the Greatwall kinase pathway or Cyclin B

Hegarat, N., Crncec, A., Suarez Peredoa Rodriguez, M. F., Iturra, F. E., Gu, Y., Busby, O., Lang, P. F., Barr, A. R., Bakal, C., Kanemaki, M. T., Lamond, A. I., Novak, B., Ly, T. & Hochegger, H., 2 Jun 2020, In : EMBO Journal. 39, 11, p. 1-23 23 p., e104419.

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Direct High-Throughput Screening Assay for mRNA Cap Guanine-N7 Methyltransferase Activity

Kasprzyk, R., Fido, M., Mamot, A., Wanat, P., Smietanski, M., Kopcial, M., Cowling, V., Kowalska, J. & Jemielity, J., 7 Apr 2020, In : Chemistry: a European Journal.

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Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes

Alabert, C., Loos, C., Voelker-Albert, M., Graziano, S., Forné, I., Reveron-Gomez, N., Schuh, L., Hasenauer, J., Marr, C., Imhof, A. & Groth, A., 28 Jan 2020, In : Cell Reports. 30, 4, p. 1223-1234.e8 21 p.

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HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6

D'Ignazio, L., Shakir, D., Batie, M., Muller, H. A. & Rocha, S., 24 Apr 2020, In : International Journal of Molecular Sciences. 21, 8, p. 1-19 19 p., 3000.

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Mutational signatures are jointly shaped by DNA damage and repair

Volkova, N. V., Meier, B., González-Huici, V., Bertolini, S., Gonzalez, S., Vöhringer, H., Abascal, F., Martincorena, I., Campbell, P. J., Gartner, A. & Gerstung, M., 1 May 2020, In : Nature Communications. 11, p. 1-15 15 p., 2169.

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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J. & Simpson, G. G., 14 Jan 2020, In : eLife. 9, p. 1-35 35 p., e49658.

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Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging

Zdańkowski, P., Trusiak, M., McGloin, D. & Swedlow, J. R., 28 Jan 2020, In : ACS Nano. 14, 1, p. 394-405 12 p.

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1 Citation (Scopus)

O-GlcNAcase contributes to cognitive function in Drosophila

Muha, V., Fenckova, M., Ferenbach, A., Catinozzi, M., Eidhof, I., Storkebaum, E., Schenck, A. & van Aalten, D., 26 Jun 2020, In : Journal of Biological Chemistry. 295, 26, p. 8636-8646 12 p.

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PALB2 chromatin recruitment restores homologous recombination in BRCA1-deficient cells depleted of 53BP1

Belotserkovskaya, R., Raga Gil, E., Lawrence, N., Butler, R., Clifford, G., Wilson, M. D. & Jackson, S. P., 10 Feb 2020, In : Nature Communications. 11, p. 1-11 11 p., 819.

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Phosphoproteomics identifies a bimodal EPHA2 receptor switch that promotes embryonic stem cell differentiation

Fernandez-Alonso, R., Bustos, F., Budzyk, M., Kumar, P., Helbig, A. O., Hukelmann, J., Lamond, A. I., Lanner, F., Zhou, H., Petsalaki, E. & Findlay, G. M., 13 Mar 2020, In : Nature Communications. 11, 1, p. 1-13 13 p., 1357.

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Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases

Mathur, S., Fletcher, A. J., Branigan, E., Hay, R. T. & Virdee, S., 16 Jan 2020, In : Cell Chemical Biology. 27, 1, p. 74-82.e6 16 p.

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Quantitative profiling of the human substantia nigra proteome from laser-capture microdissected FFPE tissue

Griesser, E., Wyatt, H., Ten Have, S., Stierstorfer, B., Lenter, M. & Lamond, A. I., 1 May 2020, In : Molecular & Cellular Proteomics. 19, 5, p. 839-851 13 p.

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Targeting a critical step in fungal hexosamine biosynthesis

Lockhart, D., Stanley, M., Raimi, O., Robinson, D., Boldovjakova, D., Squair, D., Ferenbach, A., Fang, W. & van Aalten, D., 26 Jun 2020, In : Journal of Biological Chemistry. 295, 26, p. 8678-8691 15 p.

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The Identification of Potential Therapeutic Targets for Cutaneous Squamous Cell Carcinoma

McHugh, A., Fernandes, K., Chinner, N., Ibrahim, A. F. M., Garg, A. K., Boag, G., Hepburn, L. A., Proby, C. M., Leigh, I. M. & Saville, M. K., Jun 2020, In : Journal of Investigative Dermatology. 140, 6, p. 1154-1165.e5 17 p.

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The Proteasomal Deubiquitinating Enzyme PSMD14 Regulates Macroautophagy by Controlling Golgi-to-ER Retrograde Transport

Bustamante, H. A., Cereceda, K., González, A. E., Valenzuela, G. E., Cheuquemilla, Y., Hernández, S., Arias-Muñoz, E., Cerda-Troncoso, C., Bandau, S., Soza, A., Kausel, G., Kerr, B., Mardones, G. A., Cancino, J., Hay, R. T., Rojas-Fernandez, A. & Burgos, P. V., 23 Mar 2020, In : Cells. 9, 3, p. 1-24 24 p., 777.

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Ubiquitin transfer by a RING E3 ligase occurs from a closed E2~ubiquitin conformation

Branigan, E., Penedo, J. C. & Hay, R., 5 Jun 2020, In : Nature Communications. 11, 1, p. 1-11 11 p., 2846.

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Viral DNA Binding Protein SUMOylation Promotes PML Nuclear Body Localization Next to Viral Replication Centers

Stubbe, M., Mai, J., Paulus, C., Stubbe, H. C., Berscheminski, J., Karimi, M., Hofmann, S., Weber, E., Hadian, K., Hay, R., Groitl, P., Nevels, M., Dobner, T. & Schreiner, S., 17 Mar 2020, In : MBio. 11, 2, p. 1-21 21 p., e00049-20.

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Widespread arginine phosphorylation in human cells–a novel protein PTM revealed by mass spectrometry

Fu, S., Fu, C., Zhou, Q., Lin, R., Ouyang, H., Wang, M., Sun, Y., Liu, Y. & Zhao, Y., 1 Mar 2020, In : Science China Chemistry. 63, 3, p. 341-346 6 p.

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Zooming in on Chromosome Dynamics

Eykelenboom, J. K. & Tanaka, T. U., 17 Jun 2020, In : Cell Cycle. 19, 12, p. 1422-1432 11 p.

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2019

A missense mutation in the catalytic domain of O-GlcNAc transferase links perturbations in protein O-GlcNAcylation to X-linked intellectual disability

Pravata, V. M., Gundogdu, M., Bartual, S. G., Ferenbach, A. T., Stavridis, M., Õunap, K., Pajusalu, S., Žordania, R., Wojcik, M. H. & van Aalten, D. M. F., 7 Nov 2019, In : FEBS Letters.

Research output: Contribution to journalArticle

2 Citations (Scopus)

An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity

Schmidt, N., Domingues, P., Golebiowski, F., Patzina, C., Tatham, M. H., Hay, R. T. & Hale, B. G., 27 Aug 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17399-17408 10 p.

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6 Citations (Scopus)
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Antigen receptor control of methionine metabolism in T cells

Sinclair, L. V., Howden, A., Brenes Murillo, A., Spinelli, L., Hukelmann, J., Macintyre, A. N., Liu, X., Thomson, S., Taylor, P., Rathmell, J. C., Locasale, J. W., Lamond, A. & Cantrell, D. A., 27 Mar 2019, In : eLife. 8, p. 1-29 29 p., e44210.

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14 Citations (Scopus)
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APETALA2 control of barley internode elongation

Patil, V., McDermott, H. I., Mcallister, T., Cummins, M., Clara Silva, J., Mollison, E., Meikle, R., Morris, J. A., Hedley, P. E., Waugh, R., Dockter, C., Hansson, M. & McKim, S., 12 Jun 2019, In : Development. 146, 11, 16 p., 170373.

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3 Citations (Scopus)
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11 Citations (Scopus)
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BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

Farnaby, W., Koegl, M., Roy, M. J., Whitworth, C., Diers, E., Trainor, N., Zollman, D., Steurer, S., Karolyi-Oezguer, J., Riedmueller, C., Gmaschitz, T., Wachter, J., Dank, C., Galant, M., Sharps, B., Rumpel, K., Traxler, E., Gerstberger, T., Schnitzer, R., Petermann, O. & 17 others, Greb, P., Weinstabl, H., Bader, G., Zoephel, A., Weiss-Puxbaum, A., Ehrenhöfer-Wölfer, K., Wöhrle, S., Boehmelt, G., Rinnenthal, J., Arnhof, H., Wiechens, N., Wu, M-Y., Owen-Hughes, T., Ettmayer, P., Pearson, M., McConnell, D. B. & Ciulli, A., Jul 2019, In : Nature Chemical Biology. 15, 7, p. 672-680 9 p.

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33 Citations (Scopus)
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CAPAM: the mRNA cap adenosine N6 methyltransferase

Cowling, V., 1 Mar 2019, In : Trends in Biochemical Sciences. 44, 3, p. 183-185 3 p., 1545.

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4 Citations (Scopus)
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Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability

Pravata, V., Muha, V., Gundogdu, M., Ferenbach, A., Kakade, P., Vandadi, V., Wilmes, A. C., Borodkin, V., Joss, S., Stavridis, M. & van Aalten, D., 23 Jul 2019, In : Proceedings of the National Academy of Sciences. 116, 30, p. 14961-14970 10 p.

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5 Citations (Scopus)
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Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster

Matera, A. G., Raimer, A. C., Schmidt, C. A., Kelly, J. A., Droby, G. N., Baillat, D., Ten Have, S., Lamond, A. I., Wagner, E. J. & Gray, K. M., 1 Feb 2019, In : G3 : Genes, Genomes, Genetics. 9, 2, p. 491-503 13 p.

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4 Citations (Scopus)
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Contractile acto-myosin network on nuclear envelope remnants positions human chromosomes for mitosis

Booth, A. J. R., Yue, Z., Eykelenboom, J. K., Stiff, T., Luxton, G. W. G., Hochegger, H. & Tanaka, T., 16 Jul 2019, In : eLife. 8, p. 1-21 21 p., e46902.

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2 Citations (Scopus)
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Controlling and co-ordinating chitinase secretion in a Serratia marcescens population

Costa, M. D. A. A., Owen, R. A., Tammsalu, T., Buchanan, G., Palmer, T. & Sargent, F., Nov 2019, In : Microbiology. 165, 11, p. 1233-1244 12 p.

Research output: Contribution to journalArticle

Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA

Mourão, K., Schurch, N. J., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. & Barton, G., 7 Jun 2019, In : F1000 Research. 8, p. 1-7 7 p., 819.

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Dietary restriction improves proteostasis and increases life span through endoplasmic reticulum hormesis

Matai, L., Sarkar, G. C., Chamoli, M., Malik, Y., Kumar, S. S., Rautela, U., Jana, N. R., Chakraborty, K. & Mukhopadhyay, A., 27 Aug 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17383-17392 10 p.

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10 Citations (Scopus)
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EMSY expression affects multiple components of the skin barrier with relevance to atopic dermatitis

Elias, M. S., Wright, S. C., Remenyi, J., Abbott, J. C., Bray, S. E., Cole, C., Edwards, S., Gierlinski, M., Glok, M., McGrath, J. A., Nicholson, W. V., Paternoster, L., Prescott, A. R., Have, S. T., Whitfield, P. D., Lamond, A. I. & Brown, S. J., Aug 2019, In : Journal of Allergy and Clinical Immunology. 144, 2, p. 470-481 12 p.

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3 Citations (Scopus)
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Full volume super-resolution imaging of thick mitotic spindle using 3D AO STED microscope

McGloin, D., Swedlow, J. & Zdankowski, P., 1 Apr 2019, In : Biomedical Optics Express. 10, 4, p. 1999-2009 11 p., #352466.

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6 Citations (Scopus)
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Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation

Gorelik, A., Galan Bartual, S., Borodkin, V., Varghese, J., Ferenbach, A. & van Aalten, D., Nov 2019, In : Nature Structural & Molecular Biology. 26, 11, p. 1071-1077 7 p.

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3 Citations (Scopus)
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Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells

Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V. & Martin, C. V., 8 Aug 2019, In : BMC Research Notes. 12, p. 1-7 7 p., 494.

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Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Batie, M., Frost, J., Frost, M., Wilson, J. W., Schofield, P. & Rocha, S., 15 Mar 2019, In : Science. 363, 6432, p. 1222-1226 5 p.

Research output: Contribution to journalArticle

40 Citations (Scopus)

Identification of Endogenous Adenomatous Polyposis Coli Interaction Partners and β-Catenin-Independent Targets by Proteomics

Popow, O., Paulo, J. A., Tatham, M., Volk, M., Rojas-Fernandez, A., Loyer, N., Newton, I., Januschke, J., Haigis, K. M. & Nathke, I., Sep 2019, In : Molecular Cancer Research. 17, 9, p. 1828-1841 14 p.

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Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator

Krutyhołowa, R., Hammermeister, A., Zabel, R., Abdel-Fattah, W., Reinhardt-Tews, A., Helm, M., Stark, M. J. R., Breunig, K. D., Schaffrath, R. & Glatt, S., 21 May 2019, In : Nucleic Acids Research. 47, 9, p. 4814-4830 17 p.

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1 Citation (Scopus)
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Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis

Eykelenboom, J., Gierlinski, M., Yue, Z., Hegarat, N., Pollard, H., Fukagawa, T., Hochegger, H. & Tanaka, T., 6 May 2019, In : Journal of Cell Biology. 218, 5, p. 1531-1552 22 p.

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5 Citations (Scopus)
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Loss of CRMP2 O-GlcNAcylation leads to reduced novel object recognition performance in mice

Muha, V., Williamson, R., Hills, R., McNeilly, A., McWilliams, T. G., Alonso, J., Schimpl, M., Leney, A. C., Heck, A. J. R., Sutherland, C., Read, K., McCrimmon, R., Brooks, S. P. & van Aalten, D., 27 Nov 2019, In : Open Biology. 9, 11, p. 1-15 15 p.

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LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA

Izumikawa, K., Ishikawa, H., Yoshikawa, H., Fujiyama, S., Watanabe, A., Aburatani, H., Tachikawa, H., Hayano, T., Miura, Y., Isobe, T., Simpson, R. J., Li, L., Min, J. & Takahashi, N., 4 Nov 2019, In : Nucleic Acids Research. 47, 19, p. 10357-10372 16 p.

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Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations

Bueren-Calabuig, J., Bage, M., Cowling, V. & Pisliakov, A., 19 Sep 2019, In : Nucleic Acids Research. 47, 16, p. 8675-8692 18 p., gkz613.

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