Gene Regulation and Expression

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2013

Decoding the SUMO signal

Hay, R. T., Apr 2013, In : Biochemical Society Transactions. 41, 2, p. 463-473 11 p.

Research output: Contribution to journalArticle

75 Citations (Scopus)

Deficiency of terminal ADP-ribose protein glycohydrolase TARG1/C6orf130 in neurodegenerative disease

Sharifi, R., Morra, R., Appel, C. D., Tallis, M., Chioza, B., Jankevicius, G., Simpson, M. A., Matic, I., Ozkan, E., Golia, B., Schellenberg, M. J., Weston, R., Williams, J. G., Rossi, M. N., Galehdari, H., Krahn, J., Wan, A., Trembath, R. C., Crosby, A. H., Ahel, D. & 5 others, Hay, R., Ladurner, A. G., Timinszky, G., Williams, R. S. & Ahel, I., 2 May 2013, In : EMBO Journal. 32, 9, p. 1225-1237 13 p.

Research output: Contribution to journalArticle

163 Citations (Scopus)

Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template

Neelsen, K. J., Zanini, I. M. Y., Mijic, S., Herrador, R., Zellweger, R., Chaudhuri, A. R., Creavin, K., Blow, J. J. & Lopes, M., 1 Dec 2013, In : Genes and Development. 27, 23, p. 2537-2542 6 p.

Research output: Contribution to journalArticle

48 Citations (Scopus)

DNA-binding regulates site-specific ubiquitination of IRF-1

Landré, V., Pion, E., Narayan, V., Xirodimas, D. P. & Ball, K. L., 1 Feb 2013, In : Biochemical Journal. 449, 3, p. 707-717 11 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant

Earnshaw, W. C., Allshire, R. C., Black, B. E., Bloom, K., Salmon, E. D., Brinkley, B. R., Brown, W., Cheeseman, I. M., Choo, K. H. A., Copenhaver, G. P., DeLuca, J. G., Luger, K., Desai, A., Oegema, K., Cleveland, D. W., Diekmann, S., Erhardt, S., Fitzgerald-Hayes, M., Foltz, D., Fukagawa, T. & 37 others, Gassmann, R., Maiato, H., Gerlich, D. W., Glover, D. M., Gorbsky, G. J., Harrison, S. C., Heun, P., Hirota, T., Jansen, L. E. T., Karpen, G., Kops, G. J. P. L., Lampson, M. A., Lens, S. M., Losada, A., Maddox, P. S., Margolis, R. L., Masumoto, H., McAinsh, A. D., Mellone, B. G., O'Neill, R. J., Meraldi, P., Musacchio, A., Scott, K. C., Sullivan, B. A., Straight, A. F., Stukenberg, P. T., Sullivan, K. F., Sunkel, C. E., Swedlow, J. R., Walczak, C. E., Warburton, P. E., Westermann, S., Willard, H. F., Wordeman, L., Yanagida, M., Yen, T. J. & Yoda, K., 2013, In : Chromosome Research. 21, 2, p. 101-106 6 p.

Research output: Contribution to journalArticle

Open Access
28 Citations (Scopus)

FMN2 is a novel regulator of the cyclin-dependent kinase inhibitor p21

Yamada, K., Ono, M., Bensaddek, D., Lamond, A. I. & Rocha, S., 1 Aug 2013, In : Cell cycle (Georgetown, Tex.). 12, 15, p. 2348-2354 7 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Global subcellular characterization of protein degradation using quantitative proteomics

Larance, M., Ahmad, Y., Kirkwood, K. J., Ly, T. & Lamond, A. I., Mar 2013, In : Molecular & Cellular Proteomics. 12, 3, p. 638-650 13 p.

Research output: Contribution to journalArticle

75 Citations (Scopus)

HIF-independent role of prolyl hydroxylases in the cellular response to amino acids

Durán, R. V., Mackenzie, E. D., Boulahbel, H., Frezza, C., Heiserich, L., Tardito, S., Bussolati, O., Rocha, S., Hall, M. N. & Gottlieb, E., 19 Sep 2013, In : Oncogene. 32, 38, p. 4549-4556 8 p.

Research output: Contribution to journalArticle

62 Citations (Scopus)

Identification and functional characterization of FMN2: a regulator of the cyclin-dependent kinase Inhibitor p21

Yamada, K., Ono, M., Perkins, N. D., Rocha, S. & Lamond, A. I., Mar 2013, In : Molecular Cell. 49, 5, p. 922-933 12 p.

Research output: Contribution to journalArticle

32 Citations (Scopus)

Insights into Diphthamide, key Diphtheria Toxin effector

Abdel-Fattah, W., Scheidt, V., Uthman, S., Stark, M. J. R. & Schaffrath, R., 3 May 2013, In : Toxins. 5, 5, p. 958-968 11 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment

Natsume, T., Müller, C. A., Katou, Y., Retkute, R., Gierlinski, M., Araki, H., Blow, J. J., Shirahige, K., Nieduszynski, C. A. & Tanaka, T. U., 6 Jun 2013, In : Molecular Cell. 50, 5, p. 661-674 14 p.

Research output: Contribution to journalArticle

86 Citations (Scopus)

Locus-specific proteomics by TChP: targeted chromatin purification

Pourfarzad, F., Aghajanirefah, A., de Boer, E., Ten Have, S., Bryn van Dijk, T., Kheradmandkia, S., Stadhouders, R., Thongjuea, S., Soler, E., Gillemans, N., von Lindern, M., Demmers, J., Philipsen, S. & Grosveld, F., 15 Aug 2013, In : Cell Reports. 4, 3, p. 589-600 12 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)

Mcm8 and Mcm9 form a dimeric complex in Xenopus laevis egg extract that is not essential for DNA replication initiation

Gambus, A. & Blow, J. J., 15 Apr 2013, In : Cell Cycle. 12, 8, p. 1225-1232 8 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes

Narlikar, G. J., Sundaramoorthy, R. & Owen-Hughes, T., 2013, In : Cell. 154, 3, p. 490-503 14 p.

Research output: Contribution to journalArticle

297 Citations (Scopus)

miR-132/212 knockout mice reveal roles for these miRNAs in regulating cortical synaptic transmission and plasticity

Remenyi, J., van den Bosch, M. W. M., Palygin, O., Mistry, R. B., McKenzie, C., Macdonald, A., Hutvagner, G., Arthur, J. S. C., Frenguelli, B. G. & Pankratov, Y., 26 Apr 2013, In : PLoS ONE. 8, 4, 14 p., e62509.

Research output: Contribution to journalArticle

90 Citations (Scopus)

Modification of Akt by SUMO conjugation regulates alternative splicing and cell cycle

Risso, G., Pelisch, F., Pozzi, B., Mammi, P., Blaustein, M., Colman-Lerner, A. & Srebrow, A., 2013, In : Cell Cycle. 12, 19, p. 3165-3174 10 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Modulation of higher order chromatin conformation in mammalian cell nuclei can be mediated by polyamines and divalent cations

Visvanathan, A., Ahmed, K., Even-Faitelson, L., Lleres, D., Bazett-Jones, D. P. & Lamond, A. I., 2013, In : PLoS ONE. 8, 6, 16 p., e67689.

Research output: Contribution to journalArticle

36 Citations (Scopus)

PHD1 links cell-cycle progression to oxygen sensing through hydroxylation of the centrosomal protein Cep192

Moser, S. C., Bensaddek, D., Ortmann, B., Maure, J-F., Mudie, S., Blow, J. J., Lamond, A. I., Swedlow, J. R. & Rocha, S., 26 Aug 2013, In : Developmental Cell. 26, 4, p. 381-392 12 p.

Research output: Contribution to journalArticle

43 Citations (Scopus)

PICH: A DNA Translocase Specially Adapted for Processing Anaphase Bridge DNA

Biebricher, A., Hirano, S., Enzlin, J. H., Wiechens, N., Streicher, W. W., Huttner, D., Wang, L. H. C., Nigg, E. A., Owen-Hughes, T., Liu, Y., Peterman, E., Wuite, G. J. L. & Hickson, I. D., 12 Sep 2013, In : Molecular Cell. 51, 5, p. 691-701 11 p.

Research output: Contribution to journalArticle

52 Citations (Scopus)

Plant SILAC: stable-isotope labelling with amino acids of Arabidopsis seedlings for quantitative proteomics

Lewandowska, D., ten Have, S., Hodge, K., Tillemans, V., Lamond, A. I. & Brown, J. W. S., 20 Aug 2013, In : PLoS ONE. 8, 8, e72207.

Research output: Contribution to journalArticle

23 Citations (Scopus)

PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development

Martin, S. F., Falkenberg, H., Dyrlund, T. F., Khoudoli, G. A., Mageean, C. J. & Linding, R., 2 Aug 2013, In : Journal of Proteomics. 88, p. 41-46 6 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)
159 Citations (Scopus)

Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts

Newman, T. J., Mamun, M. A., Nieduszynski, C. A. & Blow, J. J., Nov 2013, In : Nucleic Acids Research. 41, 21, p. 9705-9718 14 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans

Akay, A., Craig, A., Lehrbach, N., Larance, M., Pourkarimi, E., Wright, J. E., Lamond, A., Miska, E. & Gartner, A., Nov 2013, In : Open Biology. 3, 130151.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Small RNAs derived from the 5' end of tRNA can inhibit protein translation in human cells

Sobala, A. & Hutvagner, G., Apr 2013, In : RNA Biology. 10, 4, p. 553-563 11 p.

Research output: Contribution to journalArticle

134 Citations (Scopus)

Stochastic association of neighboring replicons creates replication factories in budding yeast

Saner, N., Karschau, J., Natsume, T., Gierlinski, M., Retkute, R., Hawkins, M., Nieduszynski, C. A., Blow, J. J., de Moura, A. P. S. & Tanaka, T. U., 2013, In : Journal of Cell Biology. 202, 7, p. 1001-1012 12 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Stress Response: Anything that Doesn't Kill You Makes You Stronger

Gartner, A. & Akay, A., 18 Nov 2013, In : Current Biology. 23, 22, p. R1012-R1014 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Structural biology: Pivotal findings for a transcription machine

Zomerdijk, J., 2013, In : Nature. 502, 7473, p. 629-630 2 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Structural biology: Pivotal findings for a transcription machine

Zomerdijk, J., 31 Oct 2013, In : Nature. 502, 7473, p. 629-630 2 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Structural plasticity of histones H3–H4 facilitates their allosteric exchange between RbAp48 and ASF1

Zhang, W., Yyl, M., Ward, R., Sobott, F., Maman, J., Murthy, A., Watson, A., Fedorov, O., Bowman, A., Owen-Hughes, T., El Mkami, H., Murzina, N., Norman, D. G. & Laue, E., Jan 2013, In : Nature Structural & Molecular Biology. 20, 1, p. 29-35 7 p.

Research output: Contribution to journalArticle

38 Citations (Scopus)

Tale of two transcription factors: NF-кB and HIF crosstalk

Bandarra, D. & Rocha, S., 2013, In : OA Molecular and Cell Biology. 1, 1, p. 1-7 7 p.

Research output: Contribution to journalArticle

Open Access
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159 Downloads (Pure)

TfR1 interacts with the IKK complex and is involved in IKK-NF-kappaB signalling

Kenneth, N. S., Mudie, S., Naron, S. & Rocha, S., 2013, In : Biochemical Journal. 449, p. 275-284

Research output: Contribution to journalArticle

21 Citations (Scopus)

The amidation step of Diphthamide biosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5 interaction network

Uthman, S., Baer, C., Scheidt, V., Liu, S., Ten Have, S., Giorgini, F., Stark, M. J. R. & Schaffrath, R., 2013, In : PLoS Genetics. 9, 2, e1003334.

Research output: Contribution to journalArticle

26 Citations (Scopus)

The Geminin and Idas coiled coils preferentially form a heterodimer that inhibits Geminin function in DNA replication licensing

Caillat, C., Pefani, D-E., Gillespie, P. J., Taraviras, S., Blow, J. J., Lygerou, Z. & Perrakis, A., Nov 2013, In : Journal of Biological Chemistry. 288, 44, p. 31624-31634 11 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

The NM23-H1/H2 homolog NDK-1 is required for full activation of Ras signaling in C. elegans

Masoudi, N., Fancsalszky, L., Pourkarimi, E., Vellai, T., Alexa, A., Reményi, A., Gartner, A., Mehta, A. & Takács-Vellai, K., 15 Aug 2013, In : Development. 140, 16, p. 3486-3495 10 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability

Bett, J. S., Ibrahim, A. F. M., Garg, A. K., Kelly, V., Pedrioli, P., Rocha, S. & Hay, R. T., 15 Apr 2013, In : Biochemical Journal. 451, 2, p. 185-194 10 p., BJ20130026.

Research output: Contribution to journalArticle

30 Citations (Scopus)

Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects

Saunders, S. P., Goh, C. S. M., Brown, S. J., Palmer, C. N. A., Porter, R. M., Cole, C., Campbell, L. E., Gierlinski, M., Barton, G. J., Schneider, G., Balmain, A., Prescott, A. R., Weidinger, S., Baurecht, H., Kabesch, M., Gieger, C., Lee, Y-A., Tavendale, R., Mukhopadhyay, S., Turner, S. W. & 14 others, Madhok, V. B., Sullivan, F. M., Relton, C., Burn, J., Meggitt, S., Smith, C. H., Allen, M. A., Barker, J. N. W. N., Reynolds, N. J., Cordell, H. J., Irvine, A. D., McLean, W. H. I., Sandilands, A. & Fallon, P. G., Nov 2013, In : Journal of Allergy and Clinical Immunology. 132, 5, p. 1121-1129 9 p.

Research output: Contribution to journalArticle

81 Citations (Scopus)

Topoisomerase IIα promotes activation of RNA polymerase i transcription by facilitating pre-initiation complex formation

Ray, S., Panova, T., Miller, G., Volkov, A., Porter, A. C. G., Russell, J., Panov, K. I. & Zomerdijk, J. C. B. M., 19 Mar 2013, In : Nature Communications. 4, 1598.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Ube2W conjugates ubiquitin to α-amino groups of protein N-termini

Tatham, M. H., Plechanovova, A., Jaffray, E. G., Salmen, H. & Hay, R. T., 2013, In : Biochemical Journal. 453, 1, p. 137-145 9 p.

Research output: Contribution to journalArticle

57 Citations (Scopus)

Ubiquitylation-dependent localization of PLK1 in mitosis

Beck, J., Maerki, S., Posch, M., Metzger, T., Persaud, A., Scheel, H., Hofmann, K., Rotin, D., Pedrioli, P., Swedlow, J. R., Peter, M. & Sumara, I., 2013, In : Nature Cell Biology. 15, 4, p. 430-439 10 p.

Research output: Contribution to journalArticle

64 Citations (Scopus)

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

Lagerstedt, I., Moore, W. J., Patwardhan, A., Sanz-García, E., Best, C., Swedlow, J. R. & Kleywegt, G. J., 1 Jan 2013, In : Journal of Structural Biology. 184, 2, p. 173-181 9 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)
2012

Advancing cell biology through proteomics in space and time (PROSPECTS)

Lamond, A. I., Uhlen, M., Horning, S., Makarov, A., Robinson, C. V., Serrano, L., Hartl, F. U., Baumeister, W., Werenskiold, A. K., Andersen, J. S., Vorm, O., Linial, M., Aebersold, R. & Mann, M., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3

Research output: Contribution to journalArticle

50 Citations (Scopus)

ALDH2 mediates 5-nitrofuran activity in multiple species

Zhou, L., Ishizaki, H., Spitzer, M., Taylor, K. L., Temperley, N. D., Johnson, S. L., Brear, P., Gautier, P., Zeng, Z., Mitchell, A., Narayan, V., McNeil, E. M., Melton, D. W., Smith, T. K., Tyers, M., Westwood, N. J. & Patton, E. E., 27 Jul 2012, In : Chemistry & Biology. 19, 7, p. 883-892 10 p.

Research output: Contribution to journalArticle

27 Citations (Scopus)

A quantitative proteomic analysis of lung epithelial (A549) cells infected with 2009 pandemic influenza A virus using stable isotope labelling with amino acids in cell culture

Dove, B. K., Surtees, R., Bean, T. J. H., Munday, D., Wise, H. M., Digard, P., Carroll, M. W., Ajuh, P., Barr, J. N. & Hiscox, J. A., May 2012, In : Proteomics. 12, 9, p. 1431-1436 6 p.

Research output: Contribution to journalArticle

31 Citations (Scopus)

A quantitative spatial proteomics analysis of proteome turnover in human cells

Boisvert, F-M., Ahmad, Y., Gierlinski, M., Charrière, F., Lamont, D., Scott, M., Barton, G. & Lamond, A. I., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3, M111.011429.

Research output: Contribution to journalArticle

215 Citations (Scopus)

ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA

De Cian, A., Praly, E., Ding, F., Singh, V., Lavelle, C., Le Cam, E., Croquette, V., Pietrement, O. & Bensimon, D., 2012, In : PLoS ONE. 7, 2, p. - 13 p., e31845.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway

Larance, M., Kirkwood, K. J., Xirodimas, D. P., Lundberg, E., Uhlen, M. & Lamond, A. I., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3

Research output: Contribution to journalArticle

17 Citations (Scopus)

Cnn1 inhibits the interactions between the KMN complexes of the yeast kinetochore

Bock, L. J., Pagliuca, C., Alfieri, C., Golfieri, C., Dal Maschio, M., De Wulf, P., Kobayashi, N., Oku, Y., Tanaka, T. U., Grove, R. A., Shrestha, K., Hazbun, T. R., Oldani, A. & Bermejo, R., 2012, In : Nature Cell Biology. 14, 6, p. 614-624 11 p.

Research output: Contribution to journalArticle

64 Citations (Scopus)

Cytosolic entry of shiga-like toxin a chain from the yeast endoplasmic reticulum requires catalytically active hrd1p

Li, S., Spooner, R. A., Hampton, R. Y., Lord, J. M. & Roberts, L. M., 2012, In : PLoS ONE. 7, 7, e41119.

Research output: Contribution to journalArticle

17 Citations (Scopus)

Dormant Origins, the Licensing Checkpoint, and the Response to Replicative Stresses

McIntosh, D. & Blow, J. J., Oct 2012, In : Cold spring harbor perspectives in biology. 4, 10, 10 p., 012955.

Research output: Contribution to journalArticle

71 Citations (Scopus)