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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Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis

Meier, B., Volkova, N. V., Gerstung, M. & Gartner, A., 28 Aug 2020, In : DNA Repair. 95, 11 p., 102957.

Research output: Contribution to journalArticle

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., 2 Jul 2020, In : Molecular Cell. 79, 1, p. 155-166 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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DEPS-1 is required for piRNA-dependent silencing and PIWI condensate organisation in Caenorhabditis elegans

Man Suen, K., Braukmann, F., Butler, R., Bensaddek, D., Akay, A., Lin, C-C., Milonaitytė, D., Doshi, N., Sapetschnig, A., Lamond, A., Ladbury, J. E. & Miska, E. A., 25 Aug 2020, In : Nature Communications. 11, 1, 13 p., 4242.

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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. H., Kowalska, J. & Jemielity, J., 7 Apr 2020, In : Chemistry: a European Journal. 11 p.

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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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3 Citations (Scopus)
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Downregulation of Keap1 confers features of a fasted metabolic state

Knatko, E. V., Tatham, M. H., Zhang, Y., Castro, C., Higgins, M., Dayalan Naidu, S., Leonardi, C., de la Vega, L., Honda, T., Griffin, J. L., Hay, R. T. & Dinkova-Kostova, A. T., Oct 2020, In : iScience. 23, 10, 48 p., 101638.

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Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer

Murphy, P., Xu, Y., Rouse, S. L., Jaffray, E. G., Plechanovova, A., Matthews, S. J., Penedo, J. C. & Hay, R., 30 Jul 2020, In : Nature Communications. 11, 13 p., 3807.

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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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Human ANKLE1 is a nuclease specific for branched DNA

Song, J., Freeman, A. D. J., Knebel, A., Gartner, A. & Lilley, D. M. J., 28 Aug 2020, In : Journal of Molecular Biology. 10 p.

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LifeTime and improving European healthcare through cell-based interceptive medicine

Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., Bock, C., Bredenoord, A. L., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fernández, X. M., Figlerowicz, M., Gasser, S. M., Hubner, N., Kjems, J., Knoblich, J. A. & 30 others, Krabbe, G., Lichter, P., Linnarsson, S., Marine, J. C., Marioni, J., Marti-Renom, M. A., Netea, M. G., Nickel, D., Nollmann, M., Novak, H. R., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J. L., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F. J., Torres-Padilla, M. E., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M. & Voet, T., 7 Sep 2020, In : Nature.

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1 Citation (Scopus)

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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6 Citations (Scopus)
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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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13 Citations (Scopus)
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Native detection of protein O-GlcNAcylation by gel electrophoresis

Fu, C. & van Aalten, D. M. F., 2 Sep 2020, In : Analyst. 5 p.

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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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5 Citations (Scopus)
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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, 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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2 Citations (Scopus)
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Population-scale proteome variation in human induced pluripotent stem cells

Mirauta, B. A., Seaton, D. D., Bensaddek, D., Brenes Murillo, A., Bonder, M. J., Kilpinen, H., Stegle, O. & Lamond, A. I., 25 Aug 2020, In : eLife. 9, 22 p., e57390.

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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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Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity

Mabbitt, P. D., Loreto, A., Déry, M-A., Fletcher, A. J., Stanley, M., Pao, K-C., Wood, N. T., Coleman, M. P. & Virdee, S., 3 Aug 2020, In : Nature Chemical Biology. 29 p.

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SUMO promotes longevity and maintains mitochondrial homeostasis during ageing in Caenorhabditis elegans

Princz, A., Pelisch, F. & Tavernarakis, N., 23 Sep 2020, In : Scientific Reports. 10, 16 p., 15513.

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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 14 p.

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The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts

Culjkovic-Kraljacic, B., Skrabanek, L., Revuelta, M. V., Gasiorek, J., Cowling, V. H., Cerchietti, L. & Borden, K. L. B., 14 Oct 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 11 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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2 Citations (Scopus)
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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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TIMP-3 facilitates binding of target metalloproteinases to the endocytic receptor LRP-1 and promotes scavenging of MMP-1

Carreca, A. P., Pravatà, V. M., Markham, M., Bonelli, S., Murphy, G., Nagase, H., Troeberg, L. & Scilabra, S. D., 21 Jul 2020, In : Scientific Reports. 10, p. 1-12 12 p., 12067.

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Tools for functional dissection of site-specific O-GlcNAcylation

Gorelik, A. & van Aalten, D., 12 Jun 2020, In : RSC Chemical Biology. 12 p.

Research output: Contribution to journalArticle

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, 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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2 Citations (Scopus)

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. 594, 4, p. 717-727 11 p.

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A mouse model for functional dissection of TAB1 O-GlcNAcylation

Authier, F., Muha, V. & van Aalten, D. M. F., 27 Aug 2019, In : Wellcome Open Research. 4, 16 p., 128.

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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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14 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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20 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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13 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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48 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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5 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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7 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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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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