Gene Regulation and Expression

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2016

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)
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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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104 Citations (Scopus)
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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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8 Citations (Scopus)
315 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)
150 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)
282 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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8 Citations (Scopus)
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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)
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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)
169 Downloads (Pure)

Global membrane protein interactome analysis using in vivo crosslinking and MS-based protein correlation profiling

Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. & Lamond, A., 1 Jul 2016, In : Molecular & Cellular Proteomics. 15, 7, p. 2476-2490 15 p.

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27 Citations (Scopus)
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H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex

Saredi, G., Huang, H., Hammond, C. M., Alabert, C., Bekker-Jensen, S., Forne, I., Reverón-Gómez, N., Foster, B. M., Mlejnkova, L., Bartke, T., Cejka, P., Mailand, N., Imhof, A., Patel, D. J. & Groth, A., 22 Jun 2016, In : Nature. 534, 7609, p. 714-718 5 p.

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59 Citations (Scopus)
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7 Citations (Scopus)
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How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., Jun 2016, In : RNA: a Publication of the RNA Society. 22, 6, p. 839-851 13 p.

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202 Citations (Scopus)
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Human IFIT1 inhibits mRNA translation of rubulaviruses but not other members of the Paramyxoviridae family

Young, D. F., Andrejeva, J., Li, X., Inesta-Vaquera, F., Dong, C., Cowling, V. H., Goodbourn, S. & Randall, R. E., 15 Oct 2016, In : Journal of Virology. 90, 20, p. 9446-9456 11 p.

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15 Citations (Scopus)
146 Downloads (Pure)

Hypoxia Induced NF-κB

D'Ignazio, L. & Rocha, S., 8 Mar 2016, In : Cells. 5, 1, 8 p., 10.

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Identification of RNF168 as a PML nuclear body regulator

Shire, K., Wong, A. I., Tatham, M. H., Anderson, O. F., Ripsman, D., Gulstene, S., Moffat, J., Hay, R. T. & Frappier, L., 1 Feb 2016, In : Journal of Cell Science. 129, 3, p. 580-591 12 p.

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9 Citations (Scopus)
152 Downloads (Pure)

Inevitability and containment of replication errors for eukaryotic genome lengths spanning Megabase to Gigabase

Al Mamun, M., Albergante, L., Moreno, A., Carrington, J. T., Blow, J. & Newman, T. J., 27 Sep 2016, In : Proceedings of the National Academy of Sciences. 113, 39, p. E5765-E5774 10 p.

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12 Citations (Scopus)
433 Downloads (Pure)

Intricate macrophage-colorectal cancer cell communication in response to radiation

Pinto, A. T., Pinto, M. L., Velho, S., Pinto, M. T., Cardoso, A. P., Figueira, R., Monteiro, A., Marques, M., Seruca, R., Barbosa, M. A., Mareel, M., Oliveira, M. J. & Rocha, S., 11 Aug 2016, In : PLoS ONE. 11, 8, p. 1-20 20 p., e0160891.

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10 Citations (Scopus)
164 Downloads (Pure)

Ionizing radiation modulates human macrophages towards a pro-inflammatory phenotype preserving their pro-invasive and pro-angiogenic capacities

Teresa Pinto, A., Laranjeiro Pinto, M., Patrícia Cardoso, A., Monteiro, C., Teixeira Pinto, M., Filipe Maia, A., Castro, P., Figueira, R., Monteiro, A., Marques, M., Mareel, M., Dos Santos, S. G., Seruca, R., Adolfo Barbosa, M., Rocha, S. & JoséOliveira, M., 6 Jan 2016, In : Scientific Reports. 6, 18765.

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47 Citations (Scopus)
140 Downloads (Pure)

Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage

Maure, J. F., Moser, S. C., Jaffray, E. G., Alpi, A. F. & Hay, R. T., 17 May 2016, In : Scientific Reports. 6, 10 p., 26178.

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3 Citations (Scopus)
141 Downloads (Pure)

Mechanoaccumulative elements of the mammalian actin cytoskeleton

Schiffhauer, E. S., Luo, T., Mohan, K., Srivastava, V., Qian, X., Griffis, E. R., Iglesias, P. A. & Robinson, D. N., 6 Jun 2016, In : Current Biology. 26, 11, p. 1473-1479 7 p.

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31 Citations (Scopus)
344 Downloads (Pure)

Metadata management for high content screening in OMERO

Li, S., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Rustici, G., Tarkowska, A., Walczysko, P., Williams, E., Allan, C., Burel, J. M., Moore, J. & 1 others, Swedlow, J. R., 1 Mar 2016, In : Methods. 96, p. 27-32 6 p.

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14 Citations (Scopus)
126 Downloads (Pure)

Micro-proteomics with iterative data analysis: proteome analysis in C.elegans at the single worm level

Bensaddek, D., Narayan, V., Nicolas, A., Brenes Murillo, A., Gartner, A., Kenyon, C. & Lamond, A., 10 Feb 2016, In : Proteomics. 16, 3, p. 381-392

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13 Citations (Scopus)
128 Downloads (Pure)

Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM

Varshney, D., Petit, A-P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. & Cowling, V. H., 1 Dec 2016, In : Nucleic Acids Research. 44, 21, p. 10423-10436 14 p.

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15 Citations (Scopus)
356 Downloads (Pure)

mRNA Cap methylation in pluripotency and differentiation

Grasso, L., Suska, O., Davidson, L., Gonatopoulos-Pournatzis, T., Williamson, R., Wasmus, L., Wiedlich, S., Peggie, M., Stavridis, M. P. & Cowling, V. H., 2 Aug 2016, In : Cell Reports. 16, 5, p. 1352-1365 14 p.

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12 Citations (Scopus)
182 Downloads (Pure)

MYC-dependent recruitment of RUNX1 and GATA2 on the SET oncogene promoter enhances PP2A inactivation in acute myeloid leukemia

Pippa, R., Dominguez, A., Malumbres, R., Endo, A., Arriazu, E., Marcotegui, N., Guruceaga, E. & Odero, M. D., 6 Jun 2016, In : Oncotarget. 8, p. 53989-54003 15 p.

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8 Citations (Scopus)
377 Downloads (Pure)

NF-κB and HIF crosstalk in immune responses

D'Ignazio, L., Bandarra, D. & Rocha, S., Feb 2016, In : FEBS Journal. 283, 3, p. 413-424 12 p.

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85 Citations (Scopus)
136 Downloads (Pure)

Notch and Hedgehog in the thymus/parathyroid common primordium: crosstalk in organ formation

Figueiredo, M., Silva, J. C., Santos, A. S., Proa, V., Alcobia, I., Zilhão, R., Cidadão, A. & Neves, H., 15 Oct 2016, In : Developmental Biology. 418, 2, p. 268-282 5 p.

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8 Citations (Scopus)
142 Downloads (Pure)

PML isoforms IV and V contribute to adenovirus-mediated oncogenic transformation by functionally inhibiting the tumor-suppressor p53

Wimmer, P., Berscheminski, J., Blanchette, P., Groitl, P., Branton, P. E., Hay, R. T., Dobner, T. & Schreiner, S., 7 Jan 2016, In : Oncogene. 35, p. 69-82 14 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Potent and selective chemical probe of hypoxic signaling downstream of HIF-α hydroxylation via VHL inhibition

Frost, J., Galdeano, C., Soares, P., Gadd, M. S., Grzes, K. M., Ellis, L., Epemolu, O., Shimamura, S., Bantscheff, M., Grandi, P., Read, K. D., Cantrell, D. A., Rocha, S. & Ciulli, A., 4 Nov 2016, In : Nature Communications. 7, p. 1-12 12 p., 13312.

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54 Citations (Scopus)
141 Downloads (Pure)

Probes of ubiquitin E3 ligases enable systematic dissection of parkin activation

Pao, K. C., Stanley, M., Han, C., Lai, Y. C., Murphy, P., Balk, K., Wood, N. T., Corti, O., Corvol, J. C., Muqit, M. M. K. & Virdee, S., May 2016, In : Nature Chemical Biology. 12, 5, p. 324-331 8 p.

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50 Citations (Scopus)

Protein phosphatase 2A as a therapeutic target in acute myeloid leukemia

Arriazu, E., Pippa, R. & Odero, M. D., 6 Apr 2016, In : Frontiers in Oncology. 6, APR, 78.

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20 Citations (Scopus)
178 Downloads (Pure)

Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression

Pascoal, S., Liu, X., Ly, T., Fang, Y., Rockliffe, N., Paterson, S., Shirran, S. L., Botting, C. H. & Bailey, N. W., 8 Jun 2016, In : Journal of Evolutionary Biology. 29, 6, p. 1234-1246 13 p.

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11 Citations (Scopus)

The cellular microscopy phenotype ontology

Jupp, S., Malone, J., Burdett, T., Heriche, J-K., Williams, E., Ellenberg, J., Parkinson, H. & Rustici, G., 18 May 2016, In : Journal of Biomedical Semantics. 7, 8 p., 28.

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15 Citations (Scopus)
138 Downloads (Pure)

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. & Owen-Hughes, T., 28 Mar 2016, In : PLoS Genetics.

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30 Citations (Scopus)
144 Downloads (Pure)

The cytotoxic T cell proteome and its shaping by the kinase mTOR

Hukelmann, J. L., Anderson, K. E., Sinclair, L. V., Grzes, K. M., Brenes Murillo, A., Hawkins, P. T., Stephens, L. R., Lamond, A. I. & Cantrell, D. A., Jan 2016, In : Nature Immunology. 17, 1, p. 104-112 9 p.

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83 Citations (Scopus)
214 Downloads (Pure)

The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3–H4 tetramers and Asf1–H3–H4 complexes

Hammond, C. M., Sundaramoorthy, R., Larance, M., Lamond, A., Stevens, M. A., El-Mkami, H., Norman, D. & Owen-Hughes, T., 27 Jul 2016, In : Nucleic Acids Research. 44, 13, p. 6157-6172 16 p.

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18 Citations (Scopus)
246 Downloads (Pure)

The NEDD8 inhibitor MLN4924 increases the size of the nucleolus and activates p53 through the ribosomal-Mdm2 pathway

Bailly, A., Perrin, A., Bou Malhab, L. J., Pion, E., Larance, M., Nagala, M., Smith, P., O'Donohue, M-F., Gleizes, P-E., Zomerdijk, J., Lamond, A. I. & Xirodimas, D. P., 28 Jan 2016, In : Oncogene. 35, 4, p. 415-426 12 p.

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21 Citations (Scopus)
299 Downloads (Pure)

The RNA-binding proteins Zfp36l1 and Zfp36l2 enforce the Thymic β-selection checkpoint by limiting DNA damage response signaling and cell cycle progression

Vogel, K. U., Bell, L. S., Galloway, A., Ahlfors, H. & Turner, M., 1 Oct 2016, In : Journal of Immunology. 197, 7, p. 2673-2685 13 p.

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23 Citations (Scopus)
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11 Citations (Scopus)
281 Downloads (Pure)

tRNA-Derived RNA Fragments Associate with Human Multisynthetase Complex (MSC) and Modulate Ribosomal Protein Translation

Keam, S. P., Sobala, A., ten Have, S. & Hutvagner, G., 22 Nov 2016, In : Journal of Proteome Research. 16, 2, p. 413-420 8 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Ubiquitinated Fancd2 recruits Fan1 to stalled replication forks to prevent genome instability

Lachaud, C., Moreno, A., Marchesi, F., Toth, R., Blow, J. J. & Rouse, J., 19 Feb 2016, In : Science. 351, 6275, p. 846-849 4 p.

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Open Access
58 Citations (Scopus)

Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules

Krupina, K., Kleiss, C., Metzger, T., Fournane, S., Schmucker, S., Hofmann, K., Fischer, B., Paul, N., Porter, I. M., Raffelsberger, W., Poch, O., Swedlow, J. R., Brino, L. & Sumara, I., 11 Jan 2016, In : Developmental Cell. 36, 1, p. 63-78 16 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Unlocking the chromatin code by deciphering protein–DNA interactions

Bensaddek, D. & Lamond, A., Nov 2016, In : Molecular Systems Biology. 12, 11, p. 1-3 3 p., 887.

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Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

Moreno, A., Carrington, J. T., Albergante, L., Al Mamun, M., Haagensen, E. J., Komseli, E-S., Gorgoulis, V. G., Newman, T. J. & Blow, J., 27 Sep 2016, In : Proceedings of the National Academy of Sciences. 113, 39, p. E5757-E5764 8 p.

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45 Citations (Scopus)
353 Downloads (Pure)
2017

A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis

Makrantoni, V., Ciesiolka, A., Lawless, C., Fernius, J., Marston, A. L., Lydall, D. & Stark, M. J. R., 7 Sep 2017, In : G3 : Genes, Genomes, Genetics. 7, 9, p. 3203-3215 13 p.

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2 Citations (Scopus)
142 Downloads (Pure)

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Zhang, R., Calixto, C. P. G., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Entizne, J. C., Lewandowska, D., ten Have, S., Frei dit Frey, N., Hirt, H., James, A. B., Nimmo, H. G., Barta, A., Kalyna, M. & Brown, J. W. S., 19 May 2017, In : Nucleic Acids Research. 45, 9, p. 5061-5073 13 p.

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63 Citations (Scopus)
195 Downloads (Pure)

ALADIN is Required for the Production of Fertile Mouse Oocytes

Carvalhal, S., Stevense, M., Koehler, K., Naumann, R., Huebner, A., Jessberger, R. & Griffis, E. R., 17 Sep 2017, In : Molecular Biology of the Cell. 28, 19, p. 2470-2478 9 p.

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6 Citations (Scopus)
140 Downloads (Pure)

A mutant O-GlcNAcase enriches Drosophila developmental regulators

Selvan, N., Williamson, R., Mariappa, D., Campbell, D. G., Gourlay, R., Ferenbach, A. T., Aristotelous, T., Hopkins-Navratilova, I., Trost, M. & van Aalten, D. M. F., Aug 2017, In : Nature Chemical Biology. 13, 8, p. 882-887 8 p.

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17 Citations (Scopus)
162 Downloads (Pure)