Gene Regulation and Expression

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2019

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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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.

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48 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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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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6 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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Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases

Fang, W., Sanz, A. B., Galan Bartual, S., Wang, B., Ferenbach, A., Farkaš, V., Hurtado-Guerrero, R., Arroyo, J. & van Aalten, D., 10 Apr 2019, In : Nature Communications. 10, 1, p. 1-10 10 p., 1669.

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Multi-batch TMT reveals false positives, batch effects and missing values

Brenes Murillo, A., Hukelmann, J., Bensaddek, D. & Lamond, A., 1 Oct 2019, In : Molecular and Cellular Proteomics. 18, 10, p. 1967-1980 14 p.

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14 Citations (Scopus)
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Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation

Wang, Y., Tatham, M. H., Schmidt-Heck, W., Swann, C., Singh-Dolt, K., Meseguer-Ripolles, J., Lucendo-Villarin, B., Kunath, T., Rudd, T. R., Smith, A. J. H., Hengstler, J. G., Godoy, P., Hay, R. T. & Hay, D. C., 28 Jun 2019, In : iScience. 16, p. 206-217 12 p.

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5 Citations (Scopus)
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Nuclear and cytoplasmic WDR-23 isoforms mediate differential effects on GEN-1 and SKN-1 substrates

Spatola, B. N., Lo, J. Y., Wang, B. & Curran, S. P., 13 Aug 2019, In : Scientific Reports. 9, 1, p. 1-11 11 p., 11783.

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Oncogenic PIK3CA mutations increase dependency on the mRNA cap methyltransferase, RNMT, in breast cancer cells

Dunn, S., Lombardi, O., Lukoszek, R. & Cowling, V., Apr 2019, In : Open Biology. 9, 4, p. 1-15 15 p., 190052.

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2 Citations (Scopus)
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Persistent DNA Damage Foci and DNA Replication with a Broken Chromosome in the African Trypanosome

Glover, L., Marques, C., Suska, O. & Horn, D., Aug 2019, In : MBio. 10, 4, p. 1-17 17 p., e01252-19.

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5 Citations (Scopus)
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2 Citations (Scopus)
77 Downloads (Pure)
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1 Citation (Scopus)
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Publisher Correction: 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., 2 Jul 2019, In : Nature Chemical Biology. 15, 8, p. 846 1 p.

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1 Citation (Scopus)

Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P-M., Huber, W., Dietrich, S., Helin, K. & Zaugg, J. B., 3 Dec 2019, In : Cell Reports. 29, 10, p. 3147-3159.e12 26 p.

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5 Citations (Scopus)
55 Downloads (Pure)
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14 Citations (Scopus)
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Reprogramming of Trypanosoma cruzi metabolism triggered by parasite interaction with the host cell extracellular matrix

Mattos, E. C., Canuto, G., Varón, N. C. M., Magalhães, R. D. M., Crozier, T. W. M., Lamont, D. J., Tavares, M. F. M., Colli, W., Ferguson, M. A. J. & Alves, M. J. M., 6 Feb 2019, In : PLoS Neglected Tropical Diseases. 13, 2, p. 1-27 27 p., e0007103.

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4 Citations (Scopus)
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RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

Frost, J., Ciulli, A. & Rocha, S., 29 Jan 2019, In : Wellcome Open Research. 4, p. 1-17 17 p., 17.

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2 Citations (Scopus)
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SILAC-based quantitative proteomic analysis of Drosophila gastrula stage embryos mutant for fibroblast growth factor signalling

Beati, H., Langlands, A., ten Have, S. & Müller, H. -A. J., 24 Dec 2019, In : Fly. 19 p.

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2 Citations (Scopus)

Spatial-Stochastic modelling of synthetic gene regulatory networks

Macnamara, C. K., Mitchell, E. I. & Chaplain, M. A. J., 7 May 2019, In : Journal of Theoretical Biology. 468, p. 27-44 18 p.

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Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation

Rabl, J., Bunker, R. D., Schenk, A. D., Cavadini, S., Gill, M. E., Abdulrahman, W., Andrés-Pons, A., Luijsterburg, M. S., Ibrahim, A. F. M., Branigan, E., Aguirre, J. D., Marceau, A. H., Guérillon, C., Bouwmeester, T., Hassiepen, U., Peters, A. H. F. M., Renatus, M., Gelman, L., Rubin, S. M., Mailand, N. & 3 others, van Attikum, H., Hay, R. T. & Thomä, N. H., 8 Aug 2019, In : Molecular Cell. 75, 3, p. 483-497.e9 15 p.

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5 Citations (Scopus)
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Structure-Based Design of a Macrocyclic PROTAC

Testa, A., Hughes, S. J., Lucas, X., Wright, J. E. & Ciulli, A., 19 Nov 2019, In : Angewandte Chemie International Edition. 9 p.

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Sumoylation regulates protein dynamics during meiotic chromosome segregation in C. elegans oocytes

Pelisch, F., Bel Borja, L., Jaffray, E. & Hay, R., 18 Jul 2019, In : Journal of Cell Science. 132, 14, 13 p., jcs232330.

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2 Citations (Scopus)
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Ten quick tips for biocuration

Tang, Y. A., Pichler, K., Füllgrabe, A., Lomax, J., Malone, J., Munoz-Torres, M. C., Vasant, D. V., Williams, E. & Haendel, M., 2 May 2019, In : PLoS Computational Biology. 15, 5, p. 1-7 7 p., e1006906.

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TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

Rasmussen, K. D., Berest, I., Keβler, S., Nishimura, K., Simón-Carrasco, L., Vassiliou, G. S., Pedersen, M. T., Christensen, J., Zaugg, J. B. & Helin, K., Apr 2019, In : Genome Research. 29, 4, p. 564-575 12 p.

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8 Citations (Scopus)
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The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity

Bailly, A. P., Perrin, A., Serrano-Macia, M., Maghames, C., Leidecker, O., Trauchessec, H., Martinez-Chantar, M. L., Gartner, A. & Xirodimas, D. P., 1 Oct 2019, In : Cell Reports. 29, 1, p. 212-224.e8 21 p.

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3 Citations (Scopus)
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The Encyclopedia of Proteome Dynamics: The KinoViewer

Brenes Murillo, A. & Lamond, A., 15 Apr 2019, In : Bioinformatics. 35, 8, p. 1441-1442 2 p., bty823.

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3 Citations (Scopus)
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The Face of Chromatin Variants

Flaus, A. & Owen-Hughes, T., 5 Sep 2019, In : Cell. 178, 6, p. 1284-1286 3 p.

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The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance

Agger, K., Nishimura, K., Miyagi, S., Messling, J-E., Rasmussen, K. D. & Helin, K., 3 Oct 2019, In : Blood. 134, 14, p. 1154-1158 5 p.

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2 Citations (Scopus)
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The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε

Winczura, A., Appanah, R., Tatham, M. H., Hay, R. T. & De Piccoli, G., 25 Nov 2019, In : PLoS Genetics. 15, 11, p. 1-26 26 p., e1008427.

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TRIM17 and TRIM28 antagonistically regulate the ubiquitination and anti-apoptotic activity of BCL2A1

Lionnard, L., Duc, P., Brennan, M. S., Kueh, A. J., Pal, M., Guardia, F., Mojsa, B., Damiano, M. A., Mora, S., Lassot, I., Ravichandran, R., Cochet, C., Aouacheria, A., Potts, P. R., Herold, M. J., Desagher, S. & Kucharczak, J., May 2019, In : Cell Death and Differentiation. 26, p. 902-917 16 p.

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5 Citations (Scopus)
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2018

6-hydroxydopamine (6-OHDA) Oxidative Stress Assay for Observing Dopaminergic Neuron Loss in Caenorhabditis elegans

Offenburger, S-L. & Gartner, A., 20 Sep 2018, In : Bio-Protocol. 8, 18, 12 p., e3025.

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6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33

Offenburger, S-L., Ho, X. Y., Tachie-Menson, T., Coakley, S., Hilliard, M. A. & Gartner, A., 18 Jan 2018, In : PLoS Genetics. 14, 1, p. 1-27 27 p., e1007125.

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5 Citations (Scopus)
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A call for public archives for biological image data

Ellenberg, J., Swedlow, J. R., Barlow, M., Cook, C. E., Sarkans, U., Patwardhan, A., Brazma, A. & Birney, E., 30 Oct 2018, In : Nature Methods. 15, 11, p. 849-854 6 p.

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9 Citations (Scopus)
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Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication

Reverón-Gómez, N., González-Aguilera, C., Stewart-Morgan, K. R., Petryk, N., Flury, V., Graziano, S., Johansen, J. V., Jakobsen, J. S., Alabert, C. & Groth, A., 18 Oct 2018, In : Molecular Cell. 72, 2, p. 239-249.e5 16 p.

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34 Citations (Scopus)
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Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity

Pao, K-C., Wood, N. T., Knebel, A., Rafie, K., Stanley, M., Mabbitt, P. D., Sundaramoorthy, R., Hofmann, K., van Aalten, D. M. F. & Virdee, S., 11 Apr 2018, In : Nature. 556, 7701, p. 381-385 5 p.

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39 Citations (Scopus)
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AKT overactivation can suppress DNA repair via p70S6 kinase-dependent downregulation of MRE11

Piscitello, D., Varshney, D., Lilla, S., Vizioli, M. G., Reid, C., Gorbunova, V., Seluanov, A., Gillespie, D. A. & Adams, P. D., 25 Jan 2018, In : Oncogene. 37, 4, p. 427-438 12 p.

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14 Citations (Scopus)
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Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice

Loftus, R. M., Assmann, N., Kedia-Mehta, N., O'Brien, K. L., Garcia, A., Gillespie, C., Hukelmann, J. L., Oefner, P. J., Lamond, A. I., Gardiner, C. M., Dettmer, K., Cantrell, D. A., Sinclair, L. V. & Finlay, D. K., 14 Jun 2018, In : Nature Communications. 9, 1, p. 1-15 15 p., 2341.

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42 Citations (Scopus)
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Analysis of novel missense ATR mutations reveals new splicing defects underlying Seckel Syndrome

Llorens-Agost, M., Luessing, J., van Beneden, A., Eykelenboom, J., O'Reilly, D., Bicknell, L. S., Reynolds, J. J., van Koegelenberg, M., Hurles, M. E., Brady, A. F., Jackson, A. P., Stewart, G. S. & Lowndes, N. F., Dec 2018, In : Human Mutation. 39, 12, p. 1847-1853 7 p.

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2 Citations (Scopus)
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Computational Modelling of Cancer Development and Growth: Modelling at Multiple Scales and Multiscale Modelling

Szymańska, Z., Cytowski, M., Mitchell, E., Macnamara, C. K. & Chaplain, M., 1 May 2018, In : Bulletin of Mathematical Biology. 80, 5, p. 1366-1403 38 p.

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7 Citations (Scopus)

DHX15 regulates CMTR1-dependent gene expression and cell proliferation

Inesta-Vaquera, F., Chaugule, V. K., Galloway, A., Chandler, L., Rojas-Fernandez, A., Weidlich, S., Peggie, M. & Cowling, V., 18 Jun 2018, In : Life Science Alliance. 1, 3, 18 p., e201800092.

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12 Citations (Scopus)
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E1B-55K-Mediated Regulation of RNF4 SUMO-Targeted Ubiquitin Ligase Promotes Human Adenovirus Gene Expression

Müncheberg, S., Hay, R. T., Ip, W. H., Meyer, T., Weiß, C., Brenke, J., Masser, S., Hadian, K., Dobner, T. & Schreiner, S., Jul 2018, In : Journal of Virology. 92, 13, 18 p., e00164-18.

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4 Citations (Scopus)
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Effects of hypo O-GlcNAcylation on Drosophila development

Mariappa, D. N., Ferenbach, A. & van Aalten, D. M. F., 11 May 2018, In : Journal of Biological Chemistry. 293, 19, p. 7209-7221 13 p.

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5 Citations (Scopus)
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Efficient Analysis of Mammalian Polysomes in cells and tissues using Ribo Mega-SEC

Yoshikawa, H., Larance, M., Harney, D. J., Sundaramoorthy, R., Ly, T., Owen-Hughes, T. & Lamond, A. I., 10 Aug 2018, In : eLife. 7, 7, p. 1-26 26 p., e36530.

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Evidence for substrate assisted catalysis in N-acetylphosphoglucosamine mutase

Raimi, O. G., Hurtado Guerrero, R. & van Aalten, D. M. F., 16 Aug 2018, In : The Biochemical journal. 475, 15, p. 2547-2557 11 p.

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