Gene Regulation and Expression

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2012

Making sense of transcribing chromatin

Owen-Hughes, T. & Gkikopoulos, T., 1 Jan 2012, In : Current Opinion in Cell Biology.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

Allan, J., Fraser, R. M., Owen-Hughes, T. & Keszenman-Pereyra, D., 30 Mar 2012, In : Journal of Molecular Biology. 417, 3, p. 152-164 13 p.

Research output: Contribution to journalArticle

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51 Citations (Scopus)
216 Downloads (Pure)

Modulation of activation-associated host cell gene expression by the apicomplexan parasite Theileria annulata

Durrani, Z., Weir, W., Pillai, S., Kinnaird, J. & Shiels, B., 2012, In : Cellular Microbiology.

Research output: Contribution to journalArticle

16 Citations (Scopus)

OMERO: flexible, model-driven data management for experimental biology

Allan, C., Burel, J-M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., MacDonald, D., Moore, W. J., Neves, C., Patterson, A., Porter, M., Tarkowska, A., Loranger, B., Avondo, J., Lagerstedt, I., Lianas, L., Leo, S., Hands, K., Hay, R. T., Patwardhan, A. & 4 others, Best, C., Kleywegt, G. J., Zanetti, G. & Swedlow, J. R., 1 Mar 2012, In : Nature Methods. 9, 3, p. 245-253 9 p.

Research output: Contribution to journalArticle

198 Citations (Scopus)

Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors

Schor, I. E., Llères, D., Risso, G. J., Pawellek, A., Ule, J., Lamond, A. I. & Kornblihtt, A. R., 12 Nov 2012, In : PLoS ONE. 7, 11, 16 p., e48084.

Research output: Contribution to journalArticle

Open Access
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39 Citations (Scopus)
127 Downloads (Pure)

Polypyrimidine Tract Binding Protein (hnRNP I) Is Possibly a Conserved Modulator of miRNA-Mediated Gene Regulation

Engels, B., Jannot, G., Remenyi, J., Simard, M. J. & Hutvagner, G., 9 Mar 2012, In : PLoS ONE. 7, 3, p. - 11 p., e33144.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Preparation and use of Xenopus egg extracts to study DNA replication and chromatin associated proteins

Gillespie, P. J., Gambus, A. & Blow, J. J., Jun 2012, In : Methods. 57, 2, p. 203-13 11 p.

Research output: Contribution to journalArticle

36 Citations (Scopus)

Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway

Arabi, A., Ullah, K., Branca, R. M. M., Johansson, J., Bandarra, D., Haneklaus, M., Fu, J., Ariës, I., Nilsson, P., Den Boer, M. L., Pokrovskaja, K., Grandér, D., Xiao, G., Rocha, S., Lehtiö, J. & Sangfelt, O., 2012, In : Nature Communications. 3, 976.

Research output: Contribution to journalArticle

55 Citations (Scopus)

Quantitative proteomic analysis of yeast DNA replication proteins

Kubota, T., Stead, D. A., Hiraga, S., ten Have, S. & Donaldson, A. D., 2012, In : Methods (San Diego, Calif.). 57, 2, p. 196-202 7 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

Raf1 is a DCAF for the Rik1 DDB1-like protein and has separable roles in siRNA generation and chromatin modification

Buscaino, A., White, S. A., Houston, D. R., Lejeune, E., Simmer, F., de Lima Alves, F., Diyora, P. T., Bayne, E. H., Rappsilber, J., Allshire, R. C. & Urano, T., 2012, In : PLoS Genetics. 8, 2, e1002499.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Relationships between climate, water resources, land use and diffuse pollution and the significance of uncertainty in climate change

Dunn, S. M., Brown, I., Sample, J. & Post, H., 20 Apr 2012, In : Journal of Hydrology. 434-435, p. 19-35 17 p.

Research output: Contribution to journalArticle

40 Citations (Scopus)

Re-replication induced by geminin depletion occurs from G2 and is enhanced by checkpoint activation

Klotz-Noack, K., McIntosh, D., Schurch, N., Pratt, N. & Blow, J. J., 15 May 2012, In : Journal of Cell Science. 125, 10, p. 2436-2445 10 p.

Research output: Contribution to journalArticle

37 Citations (Scopus)

Scale integration: the structure and dynamics of macromolecular assemblies, cells and tissues

Swedlow, J. & Danuser, G., 1 Feb 2012, In : Current Opinion in Cell Biology. 24, 1, p. 1-3 3 p.

Research output: Contribution to journalArticle

Software tools, data structures, and interfaces for microscope imaging

Stuurman, N. & Swedlow, J. R., 1 Jan 2012, In : Cold Spring Harbor Protocols. 7, 1, p. 50-61 12 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis

Plechanovová, A., Jaffray, E. G., Tatham, M. H., Naismith, J. H. & Hay, R. T., 2012, In : Nature. 489, 7414, p. 115-120 5 p.

Research output: Contribution to journalArticle

267 Citations (Scopus)

SUMO-targeted ubiquitin E3 ligase RNF4 is required for the response of human cells to DNA damage

Yin, Y., Seifert, A., Chua, J. S., Maure, J-F., Golebiowski, F. & Hay, R. T., 1 Jun 2012, In : Genes & Development. 26, 11, p. 1196-1208 13 p.

Research output: Contribution to journalArticle

150 Citations (Scopus)

Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization

Ahmad, Y., Boisvert, F-M., Lundberg, E., Uhlen, M. & Lamond, A. I., 1 Mar 2012, In : Molecular & Cellular Proteomics. 11, 3

Research output: Contribution to journalArticle

37 Citations (Scopus)

The adenomatous polyposis Coli protein contributes to normal compaction of mitotic chromatin

Dikovskaya, D., Khoudoli, G., Newton, I. P., Chadha, G. S., Klotz, D., Visvanathan, A., Lamond, A., Swedlow, J. R. & Nathke, I. S., 2012, In : PLoS ONE. 7, 6, e38102.

Research output: Contribution to journalArticle

8 Citations (Scopus)

The dynamics of replication licensing in live Caenorhabditis elegans embryos

Sonneville, R., Querenet, M., Craig, A., Gartner, A. & Blow, J. J., 23 Jan 2012, In : Journal of Cell Biology. 196, 2, p. 233-246 14 p.

Research output: Contribution to journalArticle

Open Access
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48 Citations (Scopus)
178 Downloads (Pure)

The Function of Snodprot in the Cerato-Platanin Family from Dactylellina cionopaga in Nematophagous Fungi

Yu, H., Duan, J., Wang, B. & Jiang, X., 2012, In : Bioscience biotechnology and biochemistry. 76, 10, p. 1835-1842 8 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

The human T-lymphotropic virus type 1 tax protein inhibits nonsense-mediated mRNA decay by interacting with INT6/EIF3E and UPF1

Mocquet, V., Neusiedler, J., Rende, F., Cluet, D., Robin, J-P., Terme, J-M., Dodon, M. D., Wittmann, J., Morris, C., Le Hir, H., Ciminale, V. & Jalinot, P., 2012, In : Journal of Virology. 86, 14, p. 7530-7543 14 p.

Research output: Contribution to journalArticle

51 Citations (Scopus)

The p53 isoforms are differentially modified by Mdm2

Camus, S., Menendez, S., Fernandes, K., Kua, N., Liu, G., Xirodimas, D. P., Lane, D. P. & Bourdon, J-C., 15 Apr 2012, In : Cell Cycle. 11, 8, p. 1646-1655 10 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4

Watson, A. A., Mahajan, P., Mertens, H. D. T., Deery, M. J., Zhang, W., Chen, Y., Edlich, C., Laue, E. D., Berridge, G., Burgess-Brown, N. A., Gileadi, O., Svergun, D. I., Pham, P., Du, X., Bartke, T., Kouzarides, T., Wiechens, N. & Owen-Hughes, T., 2012, In : Journal of Molecular Biology. 422, 1, p. 3-17 15 p.

Research output: Contribution to journalArticle

42 Citations (Scopus)

The ubiquitin E1 enzyme Ube1 mediates NEDD8 activation under diverse stress conditions

Leidecker, O., Matic, I., Mahata, B., Pion, E. & Xirodimas, D. P., 15 Mar 2012, In : Cell Cycle. 11, 6, p. 1142-1150 9 p.

Research output: Contribution to journalArticle

61 Citations (Scopus)

Tratamiento exitoso de la necrosis isquémica del glande poscircuncisión con oxígeno hiperbárico y pentoxifilina intravenosa

Translated title of the contribution: Successful treatment of post circumcision glanular ischemia-necrosis with hyperbaric oxygen and intravenous pentoxifyllineElemen, L., Akay, A., Topçu, K. & Gürcan, N. I., 1 Mar 2012, In : Actas Urologicas Espanolas. 36, 3, p. 200-201 2 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Why are patients with small cell lung cancer (SCLC) not given chemotherapy?

Khan, M. I., Brown, E. J., Lord, H., Allan, C., Sim, L., Buckle, F. & Rankin, E. M., Jan 2012, In : Lung Cancer. 75, p. S59-S59 1 p.

Research output: Contribution to journalArticle

2011

Absolute SILAC-compatible expression strain allows SUMO-2 copy number determination in clinical samples

Matic, I., Jaffray, E. G., Oxenham, S. K., Groves, M. J., Barratt, C. L. R., Tauro, S., Stanley-Wall, N. R. & Hay, R. T., Oct 2011, In : Journal of Proteome Research. 10, 10, p. 4869-4875 7 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

A multiprotein binding interface in an intrinsically disordered region of the tumor suppressor protein interferon regulatory factor-1

Narayan, V., Halada, P., Hernychová, L., Chong, Y. P., Žáková, J., Hupp, T. R., Vojtesek, B. & Ball, K. L., 22 Apr 2011, In : Journal of Biological Chemistry. 286, 16, p. 14291-14303 13 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA

Moore, H. C., Johnston, M., Nicol, S. M., Bourdon, J-C., Thompson, A. M., Hutvagner, G. & Fuller-Pace, F. V., Apr 2011, In : RNA: a Publication of the RNA Society. 17, 4, p. 555-562 8 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

An intranucleolar body associated with rDNA

Hutten, S., Prescott, A., James, J., Riesenberg, S., Boulon, S., Lam, Y. W. & Lamond, A. I., Oct 2011, In : Chromosoma. 120, 5, p. 481-499 19 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

A novel reporter of notch signalling indicates regulated and random notch activation during vertebrate neurogenesis

Vilas-Boas, F., Fior, R., Swedlow, J. R., Storey, K. G. & Henrique, D., 31 Aug 2011, In : BMC Molecular Biology. 9, p. - 16 p., 58.

Research output: Contribution to journalArticle

27 Citations (Scopus)

Antagonistic crosstalk between APC and HIF-1 alpha

Nathke, I. & Rocha, S., 15 May 2011, In : Cell Cycle. 10, 10, p. 1545-1547 3 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization

Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J. L., Barton, G. J. & Owen-Hughes, T., 23 Sep 2011, In : Science. 333, 6050, p. 1758-1760 3 p.

Research output: Contribution to journalArticle

174 Citations (Scopus)

A role for SUMOylation in snoRNP biogenesis revealed by quantitative proteomics

Westman, B. J. & Lamond, A. I., 1 Jan 2011, In : Nucleus. 2, 1, p. 30-37 8 p.

Research output: Contribution to journalArticle

15 Citations (Scopus)

A Screen for Novel Phosphoinositide 3-kinase Effector Proteins

Dixon, M. J., Gray, A., Boisvert, F-M., Agacan, M., Morrice, N. A., Gourlay, R., Leslie, N. R., Downes, C. P. & Batty, I. H., Apr 2011, In : Molecular & Cellular Proteomics. 10, 4, p. - 13 p., 003178.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Biphasic chromatin binding of histone chaperone FACT during eukaryotic chromatin DNA replication

Kundu, L. R., Seki, M., Watanabe, N., Murofushi, H., Furukohri, A., Waga, S., Score, A. J., Blow, J. J., Horikoshi, M., Enomoto, T. & Tada, S., Jun 2011, In : Biochimica et Biophysica Acta. Molecular Cell Research. 1813, 6, p. 1129-1136 8 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

CDC-48/p97 Coordinates CDT-1 Degradation with GINS Chromatin Dissociation to Ensure Faithful DNA Replication

Franz, A., Orth, M., Pirson, P. A., Sonneville, R., Blow, J. J., Gartner, A., Stemmann, O. & Hoppe, T., 7 Oct 2011, In : Molecular Cell. 44, 1, p. 85-96 12 p.

Research output: Contribution to journalArticle

60 Citations (Scopus)

Comparative proteomic analysis identifies a role for SUMO in protein quality control

Tatham, M. H., Matic, I., Mann, M. & Hay, R. T., 21 Jun 2011, In : Science Signaling. 4, 178, p. - 12 p., rs4.

Research output: Contribution to journalArticle

125 Citations (Scopus)

Comparison of bipolar electrosurgical devices with ligatures and endoclips in the rat appendicitis model

Elemen, L., Yazir, Y., Akay, A., Boyacioǧlu, Z., Ceyran, B. & Ceylan, S., 2011, In : Journal of Pediatric Surgery. 46, 10, p. 1923-1929 7 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

DNA repair factor APLF is a histone chaperone

Mehrotra, P. V., Ahel, D., Ryan, D. P., Weston, R., Wiechens, N., Kraehenbuehl, R., Owen-Hughes, T. & Ahel, I., 7 Jan 2011, In : Molecular Cell. 41, 1, p. 46-55 10 p.

Research output: Contribution to journalArticle

90 Citations (Scopus)

Docking-dependent ubiquitination of the interferon regulatory factor-1 tumor suppressor protein by the ubiquitin ligase CHIP

Narayan, V., Pion, E., Landré, V., Müller, P. & Ball, K. L., 7 Jan 2011, In : Journal of Biological Chemistry. 286, 1, p. 607-619 13 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Erratum: Further insights into the mechanism of hypoxia-induced NFκB (Cell Cycle (2011) 10 (879-82))

Melvin, A., Mudie, S. & Rocha, S., 2011, In : Cell Cycle. 10, 12, p. 2041 1 p.

Research output: Contribution to journalArticle

Evidence for a mammalian late-G1 phase inhibitor of replication licensing distinct from geminin or Cdk activity

Sasaki, T., Li, A., Gillespie, P. J., Blow, J. J. & Gilbert, D. M., Sep 2011, In : Nucleus. 2, 5, p. 455-464

Research output: Contribution to journalArticle

4 Citations (Scopus)

Evolutionary conserved regulation of HIF-1 beta by NF-kappa B

van Uden, P., Kenneth, N. S., Webster, R., Muller, H. A., Mudie, S. & Rocha, S., Jan 2011, In : PLoS Genetics. 7, 1, p. - 15 p., e1001285.

Research output: Contribution to journalArticle

77 Citations (Scopus)

Exo70, a subunit of the exocyst complex, interacts with SNEVhPrp19/hPso4 and is involved in pre-mRNA splicing

Dellago, H., Löscher, M., Ajuh, P., Ryder, U., Kaisermayer, C., Grillari-Voglauer, R., Fortschegger, K., Gross, S., Gstraunthaler, A., Borth, N., Eisenhaber, F., Lamond, A. I. & Grillari, J., 15 Aug 2011, In : Biochemical Journal. 438, p. 81-91 11 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

From snoRNA to miRNA: Dual function regulatory non-coding RNAs

Scott, M. S. & Ono, M., 1 Nov 2011, In : Biochimie. 93, 11, p. 1987-1992 6 p.

Research output: Contribution to journalArticle

130 Citations (Scopus)

Functional interactions between ubiquitin E2 enzymes and TRIM proteins

Napolitano, L. M., Jaffray, E. G., Hay, R. T. & Meroni, G., 1 Mar 2011, In : Biochemical Journal. 434, p. 309-319 11 p.

Research output: Contribution to journalArticle

63 Citations (Scopus)

HIF-1 alpha depletion results in SP1-mediated cell cycle disruption and alters the cellular response to chemotherapeutic drugs

Culver, C., Melvin, A., Mudie, S. & Rocha, S., 15 Apr 2011, In : Cell Cycle. 10, 8, p. 1249-1260 12 p.

Research output: Contribution to journalArticle

28 Citations (Scopus)

How to be a mitotic chromosome

Moser, S. C. & Swedlow, J. R., Apr 2011, In : Chromosome Research. 19, 3, p. 307-319 13 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Identification of human miRNA precursors that resemble box C/D snoRNAs

Ono, M., Scott, M. S., Yamada, K., Avolio, F., Barton, G. J. & Lamond, A. I., May 2011, In : Nucleic Acids Research. 39, 9, p. 3879-3891 13 p.

Research output: Contribution to journalArticle

95 Citations (Scopus)