Gene Regulation and Expression

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2017
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Continued 26S proteasome dysfunction in mouse brain cortical neurons impairs autophagy and the Keap1-Nrf2 oxidative defence pathway

Ugun-Klusek, A., Tatham, M. H., Elkharaz, J., Constantin-Teodosiu, D., Lawler, K., Mohamed, H., Paine, S. M. L., Anderson, G., John Mayer, R., Lowe, J., Ellen Billett, E. & Bedford, L., Jan 2017, In : Cell Death and Disease. 8, p. 1-12 12 p., e2531.

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14 Citations (Scopus)
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Control of amino-acid transport coordinates metabolic reprogramming in T cell malignancy

Grzes, K. M., Swamy, M., Hukelmann, J. L., Emslie, E., Sinclair, L. V. & Cantrell, D. A., 26 May 2017, In : Leukemia. 31, p. 2771-2779 9 p.

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11 Citations (Scopus)
143 Downloads (Pure)

CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis

Sonneville, R., Priego Moreno, S., Knebel, A., Johnson, C., Hastie, C. J., Gartner, A., Gambus, A. & Labib, K., 3 Apr 2017, In : Nature Cell Biology. 19, p. 468-479 11 p.

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24 Citations (Scopus)
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Cutting Edge: Building bridges between cellular and molecular structural biology

Patwardhan, A., Brandt, R., Butcher, S. J., Collinson, L., Gault, D., Grünewald, K., Hecksel, C., Huiskonen, J. T., Iudin, A., Jones, M. L., Korir, P. K., Koster, A. J., Lagerstedt, I., Lawson, C. L., Mastronarde, D., McCormick, M., Parkinson, H. E., Rosenthal, P. B., Saalfeld, S., Saibil, H. R. & 7 others, Sarntivijai, S., Solanes Valero, I., Subramaniam, S., Swedlow, J. R., Tudose, I., Winn, M. & Kleywegt, G. J., 24 Jul 2017, In : eLife. 6, p. 1-11 11 p., e25835.

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6 Citations (Scopus)
113 Downloads (Pure)

Direct Monitoring of Protein O-GlcNAcylation by High-Resolution Native Mass Spectrometry

Leney, A. C., Rafie, K., Van Aalten, D. M. F. & Heck, A. J. R., 18 Aug 2017, In : ACS Chemical Biology. 12, 8, p. 2078-2084 7 p.

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6 Citations (Scopus)
142 Downloads (Pure)

Effector-Decoy Pairs: Another Countermeasure Emerging during Host-Microbe Co-evolutionary Arms Races?

Cummins, M. & Huitema, E., 1 May 2017, In : Molecular Plant. 10, 5, p. 662-664 3 p.

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1 Citation (Scopus)
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Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

Hauer, M. H., Seeber, A., Singh, V., Thierry, R., Sack, R., Amitai, A., Kryzhanovska, M., Eglinger, J., Holcman, D., Owen-Hughes, T. & Gasser, S. M., Feb 2017, In : Nature Structural & Molecular Biology. 24, 2, p. 99-107 13 p.

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76 Citations (Scopus)
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Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

Maniaci, C., Hughes, S. J., Testa, A., Chen, W., Lamont, D. J., Rocha, S., Alessi, D. R., Romeo, R. & Ciulli, A., 10 Oct 2017, In : Nature Communications. 8, p. 1-14 14 p., 830.

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58 Citations (Scopus)
186 Downloads (Pure)

Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation

Hiraga, S., Ly, T., Garzón, J., Hořejší, Z., Ohkubo, Y., Endo, A., Obuse, C., Boulton, S. J., Lamond, A. & Donaldson, A. D., 1 Mar 2017, In : EMBO Reports. 18, 3, p. 403-419 17 p.

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44 Citations (Scopus)
130 Downloads (Pure)

KDM2 family members are regulated by HIF-1 in hypoxia.

Batie, M., Druker, J., D'Ignazio, L. & Rocha, S., 17 Mar 2017, In : Cells. 6, 1, p. 1-16 16 p., 8.

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Mechanisms mitigating problems with multiple kinetochores on one microtubule in early mitosis

Yue, Z., Komoto, S., Gierlinski, M., Pasquali, D., Kitamura, E. & Tanaka, T. U., 15 Jul 2017, In : Journal of Cell Science. 130, 14, p. 2266-2276 11 p.

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Molecular mechanisms facilitating the initial kinetochore encounter with spindle microtubules

Vasileva, V., Gierlinski, M., Yue, Z., O'Reilly, N., Kitamura, E. & Tanaka, T. U., 26 Apr 2017, In : Journal of Cell Biology. 216, 6, p. 1809-1822 14 p.

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8 Citations (Scopus)
143 Downloads (Pure)

Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans

Harvald, E. B., Sprenger, R. R., Dall, K. B., Ejsing, C. S., Nielsen, R., Mandrup, S., Brenes Murillo, A., Larance, M., Gartner, A., Lamond, A. & Færgeman, N. J., 26 Jul 2017, In : Cell Systems. 5, 1, p. 38-52.e4 13 p.

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11 Citations (Scopus)
211 Downloads (Pure)

New Apex in Proteome Analysis

Ly, T. & Lamond, A. I., 28 Jun 2017, In : Cell Systems. 4, 6, p. 581-582 2 p.

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Parkin–phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity

Kumar, A., Chaugule, V. K., Condos, T. E. C., Barber, K. R., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Shaw, G. S. & Walden, H., May 2017, In : Nature Structural & Molecular Biology. 24, 5, p. 475-483 9 p.

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39 Citations (Scopus)
273 Downloads (Pure)

Poly(A)-specific ribonuclease regulates the processing of small-subunit rRNAs in human cells

Ishikawa, H., Yoshikawa, H., Izumikawa, K., Miura, Y., Taoka, M., Nobe, Y., Yamauchi, Y., Nakayama, H., Simpson, R. J., Isobe, T. & Takahashi, N., 7 Apr 2017, In : Nucleic Acids Research. 45, 6, p. 3437-3447 11 p.

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18 Citations (Scopus)
221 Downloads (Pure)

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

Nielsen, S. V., Stein, A., Dinitzen, A. B., Papaleo, E., Tatham, M. H., Poulsen, E. G., Kassem, M. M., Rasmussen, L. J., Lindorff-Larsen, K. & Hartmann-Petersen, R., 19 Apr 2017, In : PLoS Genetics. 13, 4, 26 p., e1006739.

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28 Citations (Scopus)
192 Downloads (Pure)

Prediction of protein complexes in Trypanosoma brucei by protein correlation profiling mass spectrometry and machine learning

Crozier, T. W. M., Tinti, M., Larance, M., Lamond, A. I. & Ferguson, M. A. J., 1 Dec 2017, In : Molecular & Cellular Proteomics. 16, 12, p. 2254-2267 14 p.

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6 Citations (Scopus)
170 Downloads (Pure)

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS

Ly, T., Whigham, A., Clarke, R., Brenes-Murillo, A. J., Estes, B., Madhessian, D., Lundberg, E., Wadsworth, P. & Lamond, A. I., 20 Oct 2017, In : eLife. 6, p. 1-35 35 p., e27574.

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19 Citations (Scopus)
204 Downloads (Pure)

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

Howden, A. J. M., Stam, R., Martinez Heredia, V., Motion, G. B., Hodge, K., ten Have, S., Marques Monteiro Amaro, T. M. & Huitema, E., Jul 2017, In : New Phytologist. 215, 1, p. 309-322 14 p.

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9 Citations (Scopus)
231 Downloads (Pure)

Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats

Rafie, K., Raimi, O., Ferenbach, A. T., Borodkin, V. S., Kapuria, V. & van Aalten, D. M. F., 28 Jun 2017, In : Open Biology. 7, p. 1-9 9 p., 70078.

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18 Citations (Scopus)
147 Downloads (Pure)

Reversal of DDK-mediated MCM phosphorylation by Rif1-PP1 regulates replication initiation and replisome stability independently of ATR/Chk1

Alver, R. C., Chadha, G. S., Gillespie, P. J. & Blow, J. J., 7 Mar 2017, In : Cell Reports. 18, 10, p. 2508-2520 13 p.

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36 Citations (Scopus)
163 Downloads (Pure)
Open Access
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11 Citations (Scopus)
166 Downloads (Pure)

Structural and Functional analysis of the GABARAP interaction motif (GIM)

Rogov, V. V., Stolz, A., Ravicahandran, A. C., Rios Szwed, D. O., Suzuki, H., Kniss, A., Lohr, F., Wakatsuki, S., Dotsch, V., Dikic, I., Dobson, R. C. J. & McEwan, D. G., 27 Jun 2017, In : EMBO Reports. 18, 8, p. 1382-1396 15 p., e201643587.

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60 Citations (Scopus)
236 Downloads (Pure)

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

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. & Owen-Hughes, T., 13 Apr 2017, In : eLife. 6, 28 p., e22510.

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32 Citations (Scopus)
166 Downloads (Pure)

Structure of PINK1 and mechanisms of Parkinson's disease associated mutations

Kumar, A., Tamjar, J., Waddell, A. D., Woodroof, H. I., Raimi, O. G., Shaw, A. M., Peggie, M., Muqit, M. M. K. & van Aalten, D. M. F., 9 Nov 2017, In : eLife. 6, p. 1-16 16 p., e29985.

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29 Citations (Scopus)
191 Downloads (Pure)

TDP-43 stabilises the processing intermediates of mitochondrial transcripts

Izumikawa, K., Nobe, Y., Yoshikawa, H., Ishikawa, H., Miura, Y., Nakayama, H., Nonaka, T., Hasegawa, M., Egawa, N., Inoue, H., Nishikawa, K., Yamano, K., Simpson, R. J., Taoka, M., Yamauchi, Y., Isobe, T. & Takahashi, N., 9 Aug 2017, In : Scientific Reports. 7, p. 1-14 14 p., 7709.

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17 Citations (Scopus)
154 Downloads (Pure)

The chromatin assembly factor complex 1 (CAF1) and 5-Azacytidine (5-AzaC) affect cell motility in Src-transformed human epithelial cells

Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. & Lamond, A. I., 6 Jan 2017, In : Journal of Biological Chemistry. 292, 1, p. 172-184 13 p.

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8 Citations (Scopus)
195 Downloads (Pure)

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription

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. & Miska, E. A., 7 Aug 2017, In : Developmental Cell. 42, 3, p. 241-255.e6 21 p.

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17 Citations (Scopus)
173 Downloads (Pure)

The High-Affinity Interaction between ORC and DNA that Is Required for Replication Licensing Is Inhibited by 2-Arylquinolin-4-Amines

Gardner, N. J., Gillespie, P. J., Carrington, J. T., Shanks, E. J., McElroy, S. P., Haagensen, E. J., Frearson, J. A., Woodland, A. & Blow, J. J., 17 Aug 2017, In : Cell Chemical Biology. 24, 8, p. 981-992.e4 16 p.

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5 Citations (Scopus)
142 Downloads (Pure)

The Image Data Resource: a bioimage data integration and publication platform

Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Carzo Salas, R. E. & Swedlow, J. R., Aug 2017, In : Nature Methods. 14, 8, p. 775-781 7 p.

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52 Citations (Scopus)
359 Downloads (Pure)

The Ndc80 complex targets Bod1 to human mitotic kinetochores

Schleicher, K., Porter, M., ten Have, S., Sundaramoorthy, R., Porter, I. M. & Swedlow, J. R., 15 Nov 2017, In : Open Biology. 7, p. 1-14 14 p., 170099.

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3 Citations (Scopus)
152 Downloads (Pure)

Ufd1-Npl4 recruit Cdc48 for disassembly of ubiquitylated CMG helicase at the end of chromosome replication

Maric, M., Mukherjee, P., Tatham, M. H., Hay, R. & Labib, K., 28 Mar 2017, In : Cell Reports. 18, 13, p. 3033-3042 10 p.

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11 Citations (Scopus)
211 Downloads (Pure)

Unlocking the nucleosome

Flaus, A. & Owen-Hughes, T., 20 Jan 2017, In : Science. 355, 6322, p. 245-246 2 p.

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3 Citations (Scopus)

Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator

Mehlgarten, C., Prochaska, H., Hammermeister, A., Abdel-Fattah, W., Wagner, M., Krutyhołowa, R., Jun, S. E., Kim, G-T., Glatt, S., Breunig, K. D., Stark, M. J. R. & Schaffrath, R., 5 Sep 2017, In : Toxins. 9, 9, p. 1-13 13 p.

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7 Citations (Scopus)
186 Downloads (Pure)
2016

A Generic Platform for Cellular Screening Against Ubiquitin Ligases

Maculins, T., Carter, N., Dorval, T., Hudson, K., Nissink, J. W. M., Hay, R. T. & Alwan, H., 8 Jan 2016, In : Scientific Reports. 6, 18940.

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12 Citations (Scopus)
135 Downloads (Pure)

BOD1 Is Required for Cognitive Function in Humans and Drosophila

Esmaeeli-Nieh, S., Fenckova, M., Porter, I. M., Motazacker, M. M., Nijhof, B., Castells-Nobau, A., Asztalos, Z., Weißmann, R., Behjati, F., Tzschach, A., Felbor, U., Scherthan, H., Sayfati, S. M., Ropers, H. H., Kahrizi, K., Najmabadi, H., Swedlow, J. R., Schenck, A. & Kuss, A. W., 11 May 2016, In : PLoS Genetics. 12, 5, p. 1-22 22 p., e1006022.

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8 Citations (Scopus)
128 Downloads (Pure)

BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation

Feng, Y., Vlassis, A., Roques, C., Lalonde, M. E., González-Aguilera, C., Lambert, J. P., Lee, S. B., Zhao, X., Alabert, C., Johansen, J. V., Paquet, E., Yang, X. J., Gingras, A. C., Côté, J. & Groth, A., 18 Jan 2016, In : EMBO Journal. 35, 2, p. 176-192 17 p.

Research output: Contribution to journalArticle

Open Access
42 Citations (Scopus)

CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription

Aregger, M., Kaskar, A., Varshney, D., Fernandez-Sanchez, M. E., Inesta-Vaquera, F. A., Weidlich, S. & Cowling, V. H., 3 Mar 2016, In : Molecular Cell. 61, 5, p. 734-746 13 p.

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20 Citations (Scopus)
145 Downloads (Pure)

CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells

Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. & Rocha, S., Jan 2016, In : Journal of Cell Science. 129, 1, p. 191-205 15 p.

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11 Citations (Scopus)
198 Downloads (Pure)

Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing

Galanos, P., Vougas, K., Walter, D., Polyzos, A., Maya-Mendoza, A., Haagensen, E. J., Kokkalis, A., Roumelioti, F-M., Gagos, S., Tzetis, M., Canovas, B., Igea, A., Ahuja, A. K., Zellweger, R., Havaki, S., Kanavakis, E., Kletsas, D., Roninson, I. B., Garbis, S. D., Lopes, M. & 7 others, Nebreda, A., Thanos, D., Blow, J. J., Townsend, P., Sørensen, C. S., Bartek, J. & Gorgoulis, V. G., Jul 2016, In : Nature Cell Biology. 18, 7, p. 777-789 13 p.

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105 Citations (Scopus)
594 Downloads (Pure)

Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA

Izumikawa, K., Yoshikawa, H., Ishikawa, H., Nobe, Y., Yamauchi, Y., Philipsen, S., Simpson, R. J., Isobe, T. & Takahashi, N., Nov 2016, In : Nucleic Acids Research. 44, 20, p. 9847-9859 13 p.

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Open Access
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8 Citations (Scopus)
319 Downloads (Pure)

c-Myc deregulation induces mRNA capping enzyme dependency

Lombardi, O., Varshney, D., Phillips, N. M. & Cowling, V. H., 16 Oct 2016, In : Oncotarget. 7, 50, p. 82273-82288 16 p.

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7 Citations (Scopus)
154 Downloads (Pure)

Deep Proteome Analysis Identifies Age-Related Processes in C. elegans

Narayan, V., Ly, T., Pourkarimi, E., Brenes Murillo, A., Gartner, A., Lamond, A. & Kenyon, C., 24 Aug 2016, In : Cell Systems. 3, 2, p. 144-159 15 p.

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34 Citations (Scopus)
286 Downloads (Pure)

Direct non transcriptional role of NF-Y in DNA replication

Benatti, P., Belluti, S., Miotto, B., Neusiedler, J., Dolfini, D., Drac, M., Basile, V., Schwob, E., Mantovani, R., Blow, J. J. & Imbriano, C., 1 Apr 2016, In : Biochimica et Biophysica Acta. Molecular Cell Research. 1863, 4, p. 673-685 13 p.

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Open Access
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8 Citations (Scopus)
138 Downloads (Pure)

E4 ligase-specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis

Ackermann, L., Schell, M., Pokrzywa, W., Kevei, É., Gartner, A., Schumacher, B. & Hoppe, T., Nov 2016, In : Nature Structural & Molecular Biology. 23, 11, p. 995-1002 8 p.

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12 Citations (Scopus)
730 Downloads (Pure)

Enhanced snoMEN Vectors Facilitate Establishment of GFP–HIF-1α Protein Replacement Human Cell Lines

Ono, M., Ono, K., Bensaddek, D., Afzal, V., Biddlestone, J., Ortmann, B., Mudie, S., Boivin, V., S. Scott, M., Rocha, S. & Lamond, A. I., 29 Apr 2016, In : PLoS ONE. 11, 4, 28 p., e0154759.

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1 Citation (Scopus)
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Establishment of a High-throughput Setup for Screening Small Molecules That Modulate c-di-GMP Signaling in Pseudomonas aeruginosa

Rugjee, K. N., An, S. & Ryan, R. P., 30 Jun 2016, In : JoVE: Journal of Visualized Experiments. 112, 7 p., e54115.

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2 Citations (Scopus)
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Establishment of a promoter based chromatin architecture on recently replicated DNA can accommodate variable internucleosome spacing

Fennessy, R. T. & Owen-Hughes, T., 6 Sep 2016, In : Nucleic Acids Research. 44, 15, p. 7189-7203 15 p.

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27 Citations (Scopus)
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