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Genome Integrity and Repair

The Ladies of Avignon - the birth of cubism
Group Site: 
oxford
Group Leader: 

Opher Gileadi

Group Info

Research Areas

The Genome integrity group is studying the structural biology of human disease, with a loose focus on two areas: DNA damage recognition and repair, and the impact of genetic variation on human disease.

Our DNA is continuously exposed to chemical damage, both from extraneous mutagens and from products of our own oxidative metabolism. Furthermore, the process of DNA replication in dividing cells involves intermediates such as replication forks, which have the potential to degenerate into breaks in the DNA. Most types of DNA damage are detrimental to cell survival, and all cells have highly complex mechanism of detecting and repairing DNA damage, and arresting cell division until such damage is repaired. We are investigating several classes of DNA repair proteins, primarily DNA helicases (pictured), nucleases, and polymerases. Our aim is to use structural analysis to understand the underlying mechanisms. In parallel, we are searching for small molecules that could modulate DNA repair pathways, hoping to selectively kill cancer cells based on their inherent genomic instability.

Genome-wide association studies (GWAS), sequencing of cancer genomes, and systematic expression analyses are generating a growing list of suggested links between genes and diseases. While the statistical robustness of these studies is continuously improving, a substantial fraction of the genes discovered have little-known functions or relation to diseases. To elucidate these functions and their implications, we will produce proteins involved in inflammatory and neurological diseases. The purified proteins will be used to derive structures, antibodies and activity assays.

Structures

                                                                                                                          (Click for more infornation)


Human RecQ-like DNA helicase, RECQ1                                  2V1X

Human RecQ-like DNA helicase, complex with DNA                  2WWY

Human tRNase Z, short form (ELAC1)                                      2ZWF

Human soluble guanylate cyclase, beta 3                                  2WZ1

Human MacroD1 protein                                                          2X47

Human histone H2A variant Y2, Macro domain                          2XD7

Human Amphiphysin 1, BAR domain.                                        3SOG

Human Melanoma antigen A4                                                   2WA0

Human Vaccinia-related kinase 1                                              3OP5

Catalytic domain of the heterodimeric

human soluble guanylate cyclase 1                                             3UVJ

Human LACTB2 protein                                          4AD9

Group Members
Opher Gileadi

Opher has completed his B.Sc. in Biology and Ph.D. in Biochemistry at the Hebrew University in Jerusalem. Following a postdoctoral training with Roger Kornberg at Stanford, he established a research group at the Weizmann Institute in Rehovot, Israel. Between 2001-2004 he served as chief scientist in Quantomix, Ltd. Opher joined the SGC in 2004 as head of the Biotechnology group, establishing procedures for high-throughput production of recombinant human proteins. He is now head of the Genome Integrity group. Research interests include transcription and DNA repair, protein:DNA and protein:RNA interactions technology development in protein sciences, and the impact of genetic variation on human disease.

Pavel Savitsky
Charlie Allerston

 

Charlie obtained his B.Sc. in Genetics from the University of Aberdeen, his M.Res in Bioinformatics from the University of Leeds & the University of California San Diego, and his Ph.D. in Biochemistry at University College London.  After a fellowship at University of California San Francisco he worked for Ark Therapeutics in London using X-ray crystallography and NMR in a rational drug design project targeting neuropilin-1 in the angiogenesis pathway.  Charlie joined the SGC in 2009 and pursues X-ray crystallographic studies of the metallo-beta-lactamases, Guanylate cyclases and proteins identified by Genome-wide association studies (GWAS).

Chris Cooper

Chris graduated from Merton College, University of Oxford with an M. Biochem. in Molecular and Cellular Biochemistry, before moving for a D.Phil to the Department of Engineering Science and Centre for Ecology & Hydrology (Oxford), to study DNA polymerases from thermophilic archaea. He then obtained his M.Res. in Bioinformatics at York and Uppsala Universities. He then moved back to Oxford, producing monoclonal antibodies and analysing expression of cancer (testis) antigens in human lymphomas, prior to joining the SGC Biotechnology group in 2006. Following studies on metabolic enzymes, epigenetic targets and BTB domain-containing proteins,  he joined the SGC Genome Integrity group in 2011. Research interests include DNA repair (DNA polymerases and helicases), cancer (testis) antigens, proteins identified from genetic studies and protein expression technology development.
Publications

A full, up-to-date publication list of the group can be found here

SGC:

[1]      

Keats T, Cooper CDO, Allerston CK, Phillips C, Hammarström M, Daga N, Berridge G, Mahajan P, Birgess-Brown NA, Müller S, Gräslund S, Gileadi O. (2011) Expressing the human proteome for affinity proteomics: optimizing expression of soluble protein domains and in vivo biotinylation.New Biotech, in press (doi:10.1016/j.nbt.2011.10.007)

[2]          A.T. Wang, B. Sengerova, E. Cattell, T. Inagawa, J.M. Hartley, K. Kiakos, N.A. Burgess-Brown, L.P. Swift, J.H. Enzlin, C.J. Schofield, O. Gileadi, J.A. Hartley, P.J. McHugh, Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair. Genes Dev, 25 (2011) 1859-70. Pubmed

[3]          B. Lucic, Y. Zhang, O. King, R. Mendoza-Maldonado, M. Berti, F.H. Niesen, N.A. Burgess-Brown, A.C. Pike, C.D. Cooper, O. Gileadi, A. Vindigni, A prominent beta-hairpin structure in the winged-helix domain of RECQ1 is required for DNA unwinding and oligomer formation. Nucleic Acids Res, 39 (2011) 1703-17. PMC

[4]          D. Chen, M. Vollmar, M.N. Rossi, C. Phillips, R. Kraehenbuehl, D. Slade, P.V. Mehrotra, F. von Delft, S.K. Crosthwaite, O. Gileadi, J.M. Denu, I. Ahel, Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem, 286 (2011) 13261-71. JBC

[5]          G. Berridge, R. Chalk, N. D'Avanzo, L. Dong, D. Doyle, J.I. Kim, X. Xia, N. Burgess-Brown, A. Deriso, E.P. Carpenter, O. Gileadi, High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins. Anal Biochem, 410 (2011) 272-80. PMC

[6]          A. Vindigni, F. Marino, O. Gileadi, Probing the structural basis of RecQ helicase function. Biophys Chem, 149 (2010) 67-77. ScienceDirect

[7]          P. Savitsky, J. Bray, C.D. Cooper, B.D. Marsden, P. Mahajan, N.A. Burgess-Brown, O. Gileadi, High-throughput production of human proteins for crystallization: The SGC experience. J Struct Biol, 172 (2010) 3-13. PMC

[8]          G.B. Panigrahi, M.M. Slean, J.P. Simard, O. Gileadi, C.E. Pearson, Isolated short CTG/CAG DNA slip-outs are repaired efficiently by hMutSbeta, but clustered slip-outs are poorly repaired. Proc Natl Acad Sci U S A, 107 (2010) 12593-8. PMC

[9]          A.C. Pike, B. Shrestha, V. Popuri, N. Burgess-Brown, L. Muzzolini, S. Costantini, A. Vindigni, O. Gileadi, Structure of the human RECQ1 helicase reveals a putative strand-separation pin. Proc Natl Acad Sci U S A, 106 (2009) 1039-44.PMC

[10]          B. Shrestha, C. Smee, O. Gileadi, Baculovirus expression vector system: an emerging host for high-throughput eukaryotic protein expression. Methods Mol Biol, 439 (2008) 269-89.

[11]        S. Graslund, P. Nordlund, J. Weigelt, B.M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H.W. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S.H. Kim, Z. Rao, Y. Shi, T.C. Terwilliger, C.Y. Kim, L.W. Hung, G.S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J.L. Sussman, R.C. Stevens, S.A. Lesley, I.A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M.I. Donnelly, W.H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S.K. Burley, J.S. Emtage, J.M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S.C. Almo, J.B. Bonanno, A. Fiser, S. Swaminathan, F.W. Studier, M.R. Chance, A. Sali, T.B. Acton, R. Xiao, L. Zhao, L.C. Ma, J.F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C.K. Ho, D. Wang, H. Wang, M. Jiang, G.T. Montelione, D.I. Stuart, R.J. Owens, S. Daenke, A. Schutz, U. Heinemann, S. Yokoyama, K. Bussow, K.C. Gunsalus, Protein production and purification. Nat Methods, 5 (2008) 135-46. Pubmed

[12]        O. Gileadi, N.A. Burgess-Brown, S.M. Colebrook, G. Berridge, P. Savitsky, C.E. Smee, P. Loppnau, C. Johansson, E. Salah, N.H. Pantic, High throughput production of recombinant human proteins for crystallography. Methods Mol Biol, 426 (2008) 221-46. Pubmed

[13]       B. Shrestha, C. Smee O. Gileadi,  Baculovirus expression vector system: an emerging host for high-throughput eukaryotic protein expression. Methods Mol Biol, 439 (2008) 269-89. Pubmed

[14]        N.A. Burgess-Brown, S. Sharma, F. Sobott, C. Loenarz, U. Oppermann, O. Gileadi, Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study. Protein Expr Purif, 59 (2008) 94-102. ScienceDirect

[15]        O. Gileadi, S. Knapp, W.H. Lee, B.D. Marsden, S. Muller, F.H. Niesen, K.L. Kavanagh, L.J. Ball, F. von Delft, D.A. Doyle, U.C. Oppermann, M. Sundstrom, The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins. J Struct Funct Genomics, 8 (2007) 107-19. PMC

[16]       C. Johansson, K.L. Kavanagh, O. Gileadi, U. Oppermann, Reversible sequestration of active site cysteins in a 2Fe-2S-bridged dimer provides a mechanism for glutaredoxin 2 regulation in human mitochondria. J Biol Chem, 282 (2007) 3077-82. Pubmed

 

 Pre-SGC:

 

A. Nyska, C.A. Cummings, A. Vainshtein, J. Nadler, N. Ezov, Y. Grunfeld, O. Gileadi, V. Behar, Electron microscopy of wet tissues: a case study in renal pathology. Toxicol Pathol, 32 (2004) 357-63. Pubmed

I. Barshack, J. Kopolovic, Y. Chowers, O. Gileadi, A. Vainshtein, O. Zik, V. Behar, A novel method for "Wet" SEM. Ultrastruct Pathol, 28 (2004) 29-31. Pubmed

R. Amit, O. Gileadi, J. Stavans, Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions. Proc Natl Acad Sci U S A, 101 (2004) 11605-10. Pubmed

O. Gileadi, A. Sabban, Squid sperm to clam eggs: imaging wet samples in a scanning electron microscope. Biol Bull, 205 (2003) 177-9. Pubmed

S. Thiberge, A. Nechushtan, D, Sprinzak, O. Gileadi, V. Behar, O. Zik, Y CHowers, S. Michaeli, J. Schlessinger, E. Moses, Scanning electron microscopy of cells and tissues under fully hydrated conditions. Proc. Natl Acad Sci USA, 101 (2004) 3346 - 51. Pubmed

G. Jona, L.L. Livi, O. Gileadi, Mutations in the RING domain of TFB3, a subunit of yeast transcription factor IIH, reveal a role in cell cycle progression. J Biol Chem, 277 (2002) 39409-16. Pubmed

G. Shani, S. Henis-Korenblit, G. Jona, O. Gileadi, M. Eisenstein, T. Ziv, A. Admon, A. Kimchi, Autophosphorylation restrains the apoptotic activity of DRP-1 kinase by controlling dimerization and calmodulin binding. Embo J, 20 (2001) 1099-113. Pubmed

G. Jona, B.O. Wittschieben, J.Q. Svejstrup, O. Gileadi, Involvement of yeast carboxy-terminal domain kinase I (CTDK-I) in transcription elongation in vivo. Gene, 267 (2001) 31-6. Pubmed

I. Braslavsky, R. Amit, B.M. Jaffar Ali, O. Gileadi, A. Oppenheim, J. Stavans, Objective-type dark-field illumination for scattering from microbeads. Appl Opt, 40 (2001) 5650-7. Pubmed

B.M. Ali, R. Amit, I. Braslavsky, A.B. Oppenheim, O. Gileadi, J. Stavans, Compaction of single DNA molecules induced by binding of integration host factor (IHF). Proc Natl Acad Sci U S A, 98 (2001) 10658-63. Pubmed

D. Ostapenko, O. Gileadi, Rad25p, a DNA helicase subunit of yeast transcription factor TFIIH, is required for promoter escape in vivo. Gene, 245 (2000) 109-17. Pubmed

G. Jona, M. Choder, O. Gileadi, Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochim Biophys Acta, 1491 (2000) 37-48. Pubmed

W.J. Feaver, W. Huang, O. Gileadi, L. Myers, C.M. Gustafsson, R.D. Kornberg, E.C. Friedberg, Subunit interactions in yeast transcription/repair factor TFIIH. Requirement for Tfb3 subunit in nucleotide excision repair. J Biol Chem, 275 (2000) 5941-6. Pubmed

D. Busso, A. Keriel, B. Sandrock, A. Poterszman, O. Gileadi, J.M. Egly, Distinct regions of MAT1 regulate cdk7 kinase and TFIIH transcription activities. J Biol Chem, 275 (2000) 22815-23. Pubmed

M.S. Kobor, J. Archambault, W. Lester, F.C. Holstege, O. Gileadi, D.B. Jansma, E.G. Jennings, F. Kouyoumdjian, A.R. Davidson, R.A. Young, J. Greenblatt, An unusual eukaryotic protein phosphatase required for transcription by RNA polymerase II and CTD dephosphorylation in S. cerevisiae. Mol Cell, 4 (1999) 55-62. Pubmed

M. Fridlender, Y. Sitrit, O. Shaul, O. Gileadi, A.A. Levy, Analysis of the Ac promoter: structure and regulation. Mol Gen Genet, 258 (1998) 306-14. Pubmed

F.H. Espinoza, A. Farrell, J.L. Nourse, H.M. Chamberlin, O. Gileadi, D.O. Morgan, Cak1 is required for Kin28 phosphorylation and activation in vivo. Mol Cell Biol, 18 (1998) 6365-73. Pubmed

E. Meisels, O. Gileadi, J.L. Corden, Partial truncation of the yeast RNA polymerase II carboxyl-terminal domain preferentially reduces expression of glycolytic genes. J Biol Chem, 270 (1995) 31255-61. Pubmed

W.J. Feaver, N.L. Henry, D.A. Bushnell, M.H. Sayre, J.H. Brickner, O. Gileadi, R.D. Kornberg, Yeast TFIIE. Cloning, expression, and homology to vertebrate proteins. J Biol Chem, 269 (1994) 27549-53. Pubmed

J. Rachmilewitz, O. Gileadi, T. Eldar-Geva, T. Schneider, N. de-Groot, A. Hochberg, Transcription of the H19 gene in differentiating cytotrophoblasts from human placenta. Mol Reprod Dev, 32 (1992) 196-202. Pubmed

M. Pfutz, O. Gileadi, D. Werner, Identification of human satellite DNA sequences associated with chemically resistant nonhistone polypeptide adducts. Chromosoma, 101 (1992) 609-17. Pubmed

O. Gileadi, W.J. Feaver, R.D. Kornberg, Cloning of a subunit of yeast RNA polymerase II transcription factor b and CTD kinase. Science, 257 (1992) 1389-92. Pubmed

W.J. Feaver, O. Gileadi, Y. Li, R.D. Kornberg, CTD kinase associated with yeast RNA polymerase II initiation factor b. Cell, 67 (1991) 1223-30. Pubmed

W.J. Feaver, O. Gileadi, R.D. Kornberg, Purification and characterization of yeast RNA polymerase II transcription factor b. J Biol Chem, 266 (1991) 19000-5. Pubmed

O. Gileadi, H. Lorberboum, N. de Groot, A.A. Hochberg, Location of RNase and RNase inhibitor on free cytoplasmic mRNA-protein particles from human placenta. Mol Biol Rep, 9 (1984) 241-4. Pubmed

 

Contact

opher [dot] gileadi[at]sgc [dot] ox [dot] ac [dot] uk (Dr. Opher Gileadi)

The Structural Genomics Consortium
University of Oxford
ORCRB, Roosevelt Drive
Oxford, OX3 7DQ
UK

Tel. +44 (0)1865 617572
Fax +44 (0)1865 617575

Alumni

Sebastian Latwiel (M.Sc. student)