Gene Regulation and Expression

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2016

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)
114 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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14 Citations (Scopus)
337 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)
164 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)
345 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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79 Citations (Scopus)
117 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)
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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.

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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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49 Citations (Scopus)
128 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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47 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)
163 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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14 Citations (Scopus)
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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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29 Citations (Scopus)
133 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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79 Citations (Scopus)
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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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17 Citations (Scopus)
227 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)
275 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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22 Citations (Scopus)
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11 Citations (Scopus)
260 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.

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21 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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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.

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17 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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43 Citations (Scopus)
318 Downloads (Pure)
2015

Analysis of the SUMO2 proteome during HSV-1 Infection

Sloan, E., Tatham, M. H., Groslambert, M., Glass, M., Orr, A., Hay, R. T. & Everett, R. D., 22 Jul 2015, In : PLoS Pathogens. 11, 7, 34 p., e1005059.

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26 Citations (Scopus)

Both Chromosome Decondensation and Condensation Are Dependent on DNA Replication in C.elegans Embryos

Sonneville, R., Craig, G., Labib, K., Gartner, A. & Blow, J. J., 21 Jul 2015, In : Cell Reports. 12, 3, p. 405-417 13 p.

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15 Citations (Scopus)
177 Downloads (Pure)

Cezanne regulates E2F1-dependent HIF2α expression

Moniz, S., Bandarra, D., Biddlestone, J., Campbell, K. J., Komander, D., Bremm, A. & Rocha, S., 15 Aug 2015, In : Journal of Cell Science. 128, 16, p. 3082-3093 12 p., JOCES/2015/168864.

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29 Citations (Scopus)
119 Downloads (Pure)

Collaborator of alternative reading frame protein (CARF) regulates early processing of pre-ribosomal RNA by retaining XRN2 (5′-3′ exoribonuclease) in the nucleoplasm

Sato, S., Ishikawa, H., Yoshikawa, H., Izumikawa, K., Simpson, R. J. & Takahashi, N., 2 Dec 2015, In : Nucleic Acids Research. 43, 21, p. 10397-10410 14 p.

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9 Citations (Scopus)
239 Downloads (Pure)

Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

Liu, Y., Freeman, A. D. J., Déclais, A. C., Wilson, T. J., Gartner, A. & Lilley, D. M. J., 22 Dec 2015, In : Cell Reports. 13, 11, p. 2565-2575 11 p.

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19 Citations (Scopus)
116 Downloads (Pure)

Depth Evaluation of Soft Tissue Mimicking Phantoms Using Surface Acoustic Waves

Li, C., Li, S., Wei, C., Wang, R. K. & Huang, Z., 2015, In : Physics Procedia. 63, p. 177-181 5 p.

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1 Citation (Scopus)
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Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres

Kobayashi, N., Suzuki, Y., Schoenfeld, L., Müller, C., Nieduszynski, C., Wolfe, K. & Tanaka, T., 3 Aug 2015, In : Current Biology. 25, 15, p. 2026-2033 8 p.

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17 Citations (Scopus)
174 Downloads (Pure)

Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis

Kumar, A., Aguirre, J. D., Condos, T. E. C., Martinez-Torres, R. J., Chaugule, V. K., Toth, R., Sundaramoorthy, R., Mercier, P., Knebel, A., Spratt, D. E., Barber, K. R., Shaw, G. S. & Walden, H., 14 Oct 2015, In : EMBO Journal. 34, 20, p. 2506-2521 16 p.

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84 Citations (Scopus)
333 Downloads (Pure)

Dose-dependent effects of Allopurinol on human foreskin fibroblast cell and human umbilical vein endothelial cell under hypoxia

Sun, Y., George, J. & Rocha, S., 1 Apr 2015, In : PLoS ONE. 10, 4, 12 p., e0123649.

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5 Citations (Scopus)
123 Downloads (Pure)

Evaluating the use of HILIC in large-scale, multi dimensional proteomics: horses for courses?

Bensaddek, D., Nicolas, A. & Lamond, A. I., 30 Nov 2015, In : International Journal of Mass Spectrometry. 391, p. 105-114 10 p.

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5 Citations (Scopus)
130 Downloads (Pure)

Farmers without borders-genetic structuring in century old barley (Hordeum vulgare)

Forsberg, N. E. G., Russell, J., Macaulay, M., Leino, M. W. & Hagenblad, J., Feb 2015, In : Heredity. 114, 2, p. 195-206

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13 Citations (Scopus)

Global proteomics analysis of the response to starvation in C. elegans

Larance, M., Pourkarimi, E., Wang, B., Brenes Murillo, A., Kent, R., Lamond, A. I. & Gartner, A., 1 Jul 2015, In : Molecular & Cellular Proteomics. 14, 7, p. 1989-2001 13 p.

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19 Citations (Scopus)
156 Downloads (Pure)

Global Reprogramming of Host SUMOylation during Influenza Virus Infection

Domingues, P., Golebiowski, F., Tatham, M. H., Lopes, A. M., Taggart, A., Hay, R. T. & Hale, B. G., 17 Nov 2015, In : Cell Reports. 13, 7, p. 1467-1480 14 p.

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23 Citations (Scopus)
123 Downloads (Pure)

HIF-1α, a novel piece in the NF-κB puzzle

Bandarra, D. & Rocha, S., 28 Apr 2015, In : Infammation and Cell Signaling. 2, 1, 4 p., e792.

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HIF-1α restricts NF-κB-dependent gene expression to control innate immunity signals

Bandarra, D., Biddlestone, J., Mudie, S., Müller, H. -A. J. & Rocha, S., Feb 2015, In : Disease Models & Mechanisms. 8, 2, p. 169-181 13 p.

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29 Citations (Scopus)

Kinetochore-microtubule error correction is driven by differentially regulated interaction modes

Kalantzaki, M., Kitamura, E., Zhang, T., Mino, A., Novák, B. & Tanaka, T. U., Apr 2015, In : Nature Cell Biology. 17, 4, p. 421-433 13 p.

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26 Citations (Scopus)
254 Downloads (Pure)

Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis

Rasmussen, K. D., Jia, G., Johansen, J. V., Pedersen, M. T., Rapin, N., Bagger, F. O., Porse, B. T., Bernard, O. A., Christensen, J. & Helin, K., 1 May 2015, In : Genes and Development. 29, 9, p. 910-922 13 p.

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102 Citations (Scopus)
61 Downloads (Pure)

Maintenance of distinct melanocyte populations in the interfollicular epidermis

Glover, J. D., Knolle, S., Wells, K. L., Liu, D., Jackson, I. J., Mort, R. L. & Headon, D. J., 1 Jul 2015, In : Pigment Cell and Melanoma Research. 28, 4, p. 476-480 5 p.

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14 Citations (Scopus)

Mio depletion links mTOR regulation to Aurora A and Plk1 activation at mitotic centrosomes

Platani, M., Trinkle-Mulcahy, L., Porter, M., Jeyaprakash, A. A. & Earnshaw, W. C., 6 Jul 2015, In : Journal of Cell Biology. 210, 1, p. 45-62 18 p.

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6 Citations (Scopus)

Multidimentional proteomics for cell biology

Larance, M. & Lamond, A. I., May 2015, In : Nature Reviews Molecular Cell Biology. 16, 5, p. 269-280 12 p.

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200 Citations (Scopus)
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Phosphorylation of Elp1 by Hrr25 is required for Elongator-dependent tRNA modification in yeast

Abdel-Fattah, W., Jablonowski, D., Di Santo, R., Thüring, K. L., Scheidt, V., Hammermeister, A., ten Have, S., Helm, M., Schaffrath, R. & Stark, M. J. R., 8 Jan 2015, In : PLoS Genetics. 11, 1, 16 p., e1004931.

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Open Access
23 Citations (Scopus)

Proteome-wide identification of SUMO modification sites by mass spectrometry

Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F. M., Tatham, M. H. & Hay, R. T., Sep 2015, In : Nature Protocols. 10, 9, p. 1374-1388 15 p.

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23 Citations (Scopus)

Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells

Ly, T., Endo, A. & Lamond, A. I., 2 Jan 2015, In : eLife. 2015, 4, p. 1-15 15 p., e04534.

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21 Citations (Scopus)
116 Downloads (Pure)

Proteotoxic stress reprograms the chromatin landscape of SUMO modification

Seifert, A., Schofield, P., Barton, G. & Hay, R., 7 Jul 2015, In : Science Signaling. 8, 384, p. rs7 14 p.

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33 Citations (Scopus)
178 Downloads (Pure)

Publishing and sharing multi-dimensional image data with OMERO

Burel, J-M., Besson, S., Blackburn, C., Carroll, M., Ferguson, R., Flynn, H., Gillen, K., Leigh, R., Li, S., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczysko, P., Allan, C., Moore, J. & Swedlow, J. R., Oct 2015, In : Mammalian Genome : Official Journal of the International Mammalian Genome Society. 26, 9, p. 441-447 7 p.

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9 Citations (Scopus)
159 Downloads (Pure)

Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9

Rojas-Fernandez, A., Herhaus, L., Macartney, T., Lachaud, C., Hay, R. T. & Sapkota, G. P., 29 Apr 2015, In : Scientific Reports. 5, 6 p., 9811.

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22 Citations (Scopus)
228 Downloads (Pure)