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Group interests (continued)
A major focus of the group is to combine our existing expertise with new approaches to address the biology two kinases known to orchestrate a large proportion of the cellular responses to DNA damage.
ATM and ATR are designated as phosphatidylinositol 3-kinase-related (PIK) kinases as their kinase domains are related to phospholipid kinases that phosphorylate phosphatidylinositol at the 3-position hydroxyl of the inositol ring. However, they are known to be serine and threonine directed protein kinases that are recruited to and activated by DNA. ATM is recruited to double strand breaks (DSBs) via the MRN (Mre11-Rad50-NBS1) complex. ATR, with its partner ATRIP (ATR-interacting protein), is recruited to single-stranded DNA (ssDNA) generated during DSB processing or during replication. ATM and ATR initiate signalling cascades by phosphorylating many target proteins, including Chk1 and Chk2 (checkpoint kinase 1 and 2), which initiate a secondary wave of phosphorylation events. Many other post-translation modifications required for a successful response, including, ubiquitinylation, SUMOylation, poly(ADP-ribosylation), acetylation and methylation are also dependent upon ATM and ATR.
Current projects include:
The role of the RSF1 chromatin remodelling factor in DNA double strand break (DSB) repair. Our recently published model established an early role for RSF1 in remodelling nucleosomes proximal to the break and using histone fold proteins previously implicated in centromere function as temporary placeholders required for subsequent steps in DNA repair (Figure 5, see Pessina and Lowndes 2014). In ongoing genomic and biochemical projects we are interogating this model further.
Investigating the structure and function of ATR using our novel DT40 cell line in which chicken Atr can be rapidly degraded (Figure 6, see Eykelenboom et al 2013) and replaced by epitope tagged and/or mutant forms fo Atr.- Investigating a role for ATR in cytokinesis suggested by our published work.
- Using quantitative proteomics we have identified new binding partners of ATM and ATR. Many of these have been validated and are under ongoing detailed investigation. These include an interesting class of Zinc finger containing proteins, a transcription complex and proteins previously implicated in RNA metabolism. Using gene ontology, the largest class of interactors with ATM and ATR, but not with the 53BP1 tumour suppressor, were proteins implicated in RNA biology. Characterising the precise role of selected human factors identified by our proteomic screens is a major activity within the group.
Postdoctoral, PhD and MSc Opportunities
Please email Prof Lowndes for information about opportunities for postgraduate research projects.
Lab members (Oct 2015)
Postdoctoral fellows:
Amandine Van Beneden (Belgium)
Murilo Bueno (Brazil)
Nikolay Tsanov (Bulgaria)
Jose-Luis Preito (Spain)
Graduate students:
Louise Frizzell (Ireland)
Marta Llorens-Agost (Spain)
Janna Luessing (Germany)
Chituru Okowa (Nigeria)
Irene Asensio, with Rhod Ceredig, REMEDI (Spain)
Marta Baldascini (Italy)
Stephen Murphy (Ireland)
Shideh Sakteh (Iran)
Rachel McCole (Ireland)
Lectures/ courses
1st Year Biochemistry (‘Introduction to Biochemistry’)
2nd Year Biochemistry (‘Molecular Medicine’)
2nd Year Medicine (‘Molecular Medicine’)
2nd Year Biochemistry (‘Cancer Genetics’)
3rd Year Biochemistry (‘Genomes and their organisation’)
4th Year Biochemistry (‘Advanced Chromosome Biology’ module coordinator)
Full publication list
B= Book chapter (3) R = review (21)
73. BRCA1 is required for maintenance of phosph-Chk1 and G2/M arrest during DNA crosslink repair in DT40 cells. (2015) Draga M, Madgett EB, Vandenberg CJ, du Plessis D, Kaufmann A, Werler P, Chakraborty P, Lowndes NF, Hiom K. Mol Cell Biol. In press
72. Induction of homologous recombination between sequence repeats by the activation induced cytidine deaminase (AID) protein. (2014) Buerstedde JM, Lowndes N, Schatz DG. Elife 3:e03110
71*. Rational design and validation of a Tip60 histone acetyltransferase inhibitor. (2014) Gao C, Bourke E, Scobie M, Famme MA, Koolmeister T, Helleday T, Eriksson LA, Lowndes NF, Brown JA. Sci Rep 4:5372
70*. The RSF1 histone-remodelling factor facilitates DNA double-strand break repair by recruiting centromeric and Fanconi Anaemia proteins. (2014) Pessina F, Lowndes NF. PLoS Biol. 12(5):e1001856. doi: 10.1371/journal.pbio.1001856.
69*. Hypoxia enhances the radioresistance of mouse mesenchymal stromal cells. (2014) Sugrue T, Lowndes NF, Ceredig R. Stem Cells. (8):2188-200
68*. ATR activates the S-M checkpoint during unperturbed growth to ensure sufficient replication prior to mitotic onset. (2013) Eykelenboom JK, Harte EC, Canavan L, Pastor-Peidro A, Calvo-Asensio I, Llorens-Agost M, Lowndes NF. Cell Rep. 5(4):1095-107
67*. Binding specificity of the G1/S transcriptional regulators in budding yeast. (2013) Harris, MR, Lee D, Farmer, D, Lowndes NF* & de Bruin RAM. PLoS One, Apr 4;8(4):e61059
66. Repression of G1/S transcription is mediated 1 via interaction of the GTB motif of Nrm1 and Whi5 with Swi6. (2013) Travesa A, Kalashnikova T, Robertus de Bruin R, Cass SR, Chahwan C, Lee DE, Lowndes NF & Wittenberg C. (2013) Molecular & Cellular Biology, Apr;33(8):1476-86
65*. Site-specific phosphorylation of the DNA damage mediator Rad9 by cyclin-dependent kinases, CDKs, regulates activation of Checkpoint kinase 1, Chk1. (2013) Abreu CM, Kumar, R, Hamilton D, Dawdy A, Creavin K, Eivers, S, Finn K, Balsbaugh JL, O’Connor R, Kiely PS, Shabanowitz J, Hunt DF, Grenon M & Lowndes NF*. PLoS Genetics (4): e1003310
64* R. Mesenchymal stromal cells: radio-resistant members of the bone marrow. (2013) Sugrue T, Lowndes NF*, Ceredig R. Immunol Cell Biol. Jan;91(1):5-11
63*. Co-mutation of histone H2AX S139A with Y142A rescues Y142A-induced ionizing radiation induced sensitivity. (2012) Brown, JAL, Eykelenboom, JK and Lowndes NF*. FEBS OpenBio 2, 313-317
62. Multiple Facets of The DNA Damage Response Contribute to the Radio-Resistance of Mouse Mesenchymal Stromal Cell Lines. (2012) Sugrue T, Brown JA, Lowndes NF, Ceredig R. Stem Cells 2012 Sep 7. doi: 10.1002/stem.1222. [Epub ahead of print]
61. ATR-ATRIP kinase complex triggers activation of the Fanconi anemia DNA repair pathway. (2012) Shigechi T, Tomida J, Sato K, Kobayashi M, Eykelenboom JK, Pessina F, Zhang Y, Uchida E, Ishiai M, Lowndes NF, Yamamoto K, Kurumizaka H, Maehara Y, Takata M. Cancer Res. Mar 1;72(5):1149-56.
60R. Eukaryotic DNA damage checkpoint activation in response to double-strand breaks. (2011) K. Finn, NF Lowndes, M GrenonCellular and Molecular Life Sciences. May;69(9):1447-73.
59. Modification of histones by sugar ?-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including histone H3 serine 10, and is cell cycle-regulated (2011)
Zhang S, Roche K, Nasheuer HP, Lowndes NF. J Biol Chem. Oct 28;286(43):37483-95.
58. Regulation of the DNA Damage Response and Gene Expression by the Dot1L Histone Methyltransferase and the 53Bp1 Tumour Suppressor (2011) Fitzgerald J, Moureau S, Drogaris P, O’Connell E, Abshiru N, Verreault A, Thibault P, Grenon M, Lowndes NF. PLoS One. Feb 24;6(2):e14714.
57 R. The interplay between BRCA1 and 53BP1 influences death, aging, senescence and cancer. (2010) Lowndes NF. DNA Repair (Amst). Oct 5;9(10):1112-6.
56. M. Granata, F. Lazzaro, D. Novarina, D. Panigada, F. Puddu, CM Abreu, R. Kumar, M. Grenon, NF. Lowndes, P. Plevani and M. Muzi-Falconi (2010) Dynamics of Rad9 Chromatin Binding and Checkpoint Function Are Mediated by its Dimerization and Are Cell Cycle Regulated by CDK1 Activity. PLoS Genetics, Aug 5;6(8). pii: e1001047.
55R. Rupnik A., Lowndes NF and Grenon M (2010) MRN, the race to the break. Chromosoma, 119(2):115-35.
54 B. Costelloe T. and Lowndes NF (2010) Both chromatin assembly and signalling the end of DNA repair requires acetylation of histone H3 on lysine 56. Subcell Biochem. 50:43-54.
53. Drogaris P, Le Blanc JCY, Fitzgerald J, Lowndes NF, Verreault A and Thibault P (2009) Enhanced Protein Detection Using a Trapping Mode on a Hybrid Quadrupole Linear Ion Trap (Q-Trap). Anal. Chem., Aug 1;81(15):6300-9.
52R. FitzGerald J, Grenon M, Lowndes NF (2009) 53BP1: Function and
Mechanisms of Focal Recruitment. Biochem Soc Trans. 37(Pt 4):897-904.
51. Nakahara, M, Sonoda, E, Nojima1, K, Sale, JE, Takenaka, K, Kikuchi, K, Taniguchi, Y, Nakamura, K, Sumitomo, Y, Bree, R, Lowndes, NF and Takeda, S. (2009) Genetic evidence for single-strand lesions initiating Nbs1-dependent homologous recombination in diversification of Ig V in chicken B lymphocytes. PLoS Genetics, Jan;5(1):e1000356..
50 R. Rupnik A, Grenon M, Lowndes NF (2008) Quick Guide: The MRN complex. Curr Biol. 18(11):R455-7.
49B. Dobbie IM, Lowndes NF, Sullivan KF (2008) Autofluorescent proteins. Methods Cell Biol. 85:1-22.
48 R. Roche KC and Lowndes NF (2007) An investigation into 53BP1 complex formation. Adv Exp Med Biol. 604:47-57.
47. Rossignol T, Logue ME, Reynolds K, Grenon M, Lowndes NF and Butler G (2007) Transcriptional response of Candida parapsilosis following exposure to farnesol. Antimicrob Agents Chemother. 51(7):2304-12.
46. Bree RT, Lai XY, Canavan LE, Lowndes NF (2007) Comparisons Between DT40 Wildtype and Cre1 cells as suitable model systems for studying the DNA Damage Response. Cell Cycle. Sep 15;6(18):2310-3.
45. Lowndes NF (2007) Chaperoning the Cln3 cyclin prevents promiscuous activation of start. Mol Cell. Jul 6;27(1):1-2.
44. Braet C, Stephan H, Dobbie IM, Togashi DM, Ryder AG, Foldes-Papp Z, Lowndes N, Nasheuer HP (2007) Mobility and distribution of replication protein A in living cells using fluorescence correlation spectroscopy. Exp Mol Pathol. 82(2):156-62.
43. Grenon M, Costelloe T, Jimeno S, O’Shaughnessy A, FitzGerald J, Zgheib O, Degerth L and Lowndes NF (2007) Docking onto chromatin via the S. cerevisiae Rad9 Tudor domain. Yeast. 24(2):105-19
42 R. Friedberg EC, Aguilera A, Gellert M, Hanawalt PC, Hays JB, Lehmann AR, Lindahl T, Lowndes N, Sarasin A, Wood RD. (2006) DNA repair: from molecular mechanism to human disease. DNA Repair (Amst). 5(8):986-96.
41 R. Costelloe T, Fitzgerald J, Murphy NJ, Flaus, A & Lowndes, NF Chromatin modulation and the DNA damage response. (2006). Exp Cell Res 312, 2677-86
40. Toh GW-L, O’Shaughnessy A, Jimeno S, Dobbie I, Grenon M, Maffini S, O’ Rorke A and Lowndes, NF (2006) Histone H2A phosphorylation and H3 methylation are required for a novel Rad9 DSB repair function following checkpoint activation. DNA Repair. Jun 10;5(6):693-703693-703.
39. Grenon M, Magill CP, Lowndes NF and Jackson SP (2006) Double-Strand Breaks trigger MRX- and Mec1-dependent, but Tel1-independent, checkpoint Activation. FEMS Yeast Research, 6: 836-847.
38 R. O’Shaughnessy AM, Grenon M, Gilbert C, Toh GW-L, Green CM and Lowndes NF (2006) Multiple approaches to study S. cerevisiae Rad9, a prototypical checkpoint protein. Meths. Enzym. 409: 131-150.
37. Nakamura K, Sakai W, Kawamoto T, Bree RT, Lowndes NF, Takeda S, Taniguchi Y. (2006) Genetic dissection of vertebrate 53BP1: a major role in non-homologous end joining of DNA double strand breaks. DNA Repair Jun 10;5(6):741-9.
36 R. Lowndes NF and Toh GW-L (2005) DNA repair: the importance of phosphorylating histone H2AX. Curr Biol. 15:R99-R102 .
35 R. Bree R, Neary C, Samali A and Lowndes NF (2004) The switch from survival responses to apoptosis after chromosomal breaks. DNA Repair, 3: 989-995.
34 B. Toh GW-L and Lowndes NF. (2004). DNA Damage Surveillance in Saccharomyces cerevisiae. In Eukaryotic DNA Damage Surveillance and Repair, ed. Caldecott, K., Landes Bioscience. ISBN: 1-58706-227-5.
33 R. Green CM and Lowndes NF (2004) Purification and analysis of checkpoint protein complexes from Saccharomyces cerevisiae. Methods Mol Biol. 280:291-306.
32 R. van den Bosch M and Lowndes NF. (2003) Remodelling the Rad9 checkpoint complex. Cell Cycle 3: 1-4.
31. Gilbert C, van den Bosch M. Green CM, Vialard JE, Grenon M, Erdjument-BromageH, TempstP and Lowndes NF (2003). The budding yeast Rad9 checkpoint complex: chaperone proteins are required for its function. EMBO Reports, 4: 953-958.
30 R. van den Bosch M, Bree RT and Lowndes NF. (2003) The MRN complex: coordinating and mediating the response to broken chromosomes. EMBO Reports, 4: 844-849.
29 R. Toh GW-L and Lowndes NF. (2003). Role of the Saccharomyces cerevisiae Rad9 protein in sensing and responding to DNA damage. Biochem Soc Trans., 31: 242-6.
28. Redon C, Pilch DR, Rogakou EP, Orr AH, Lowndes NF, Bonner WM. (2003)Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage. EMBO Rep. 4:678-684.
27B. de la Torre-Ruiz MA, Toh GW-L and Lowndes, NF. (2002) Budding yeast as a eukaryotic model for understanding the mechanisms of cellular responses to DNA damage. Recent Research Developments in DNA repair and Mutagenesis. Research Signpost, India 67-80 Eds: Ruiz-Rubio, Alejandre-Buran, E and Roldan-Arjona, T.
26. Chakraverty RK, Kearsey JM, Oakley TJ, Grenon M, de La Torre Ruiz MA, Lowndes NF, Hickson ID. (2001). Topoisomerase III acts upstream of Rad53p in the S-phase DNA damage checkpoint. Mol Cell. Biol., 21: 7150-7162
25. Gilbert C, Green CM and Lowndes NF (2001). Budding yeast Rad9 is an ATP-dependent Rad53 activating machine. Mol. Cell, 8:129-136.
24. Grenon M, Gilbert C, Lowndes NF. (2001) Checkpoint activation in response to double-strand breaks requires the Mre11/Rad50/Xrs2 complex. Nat. Cell Biol., 3: 844-847.
23. Yu S, Teng Y, Lowndes NF and Waters R. (2001). Inducible nucleotide excision repair of UV induced cyclobutane pyrimidine dimers in the Saccharomyces cerevisiae MFA2 gene. Mutat. Res., 485: 229-236.
22 R. Lowndes NF. (2001). DNA-damage signaling and apoptosis. Genome Biol., 2: 4028-4029.
21. Downs JA, Lowndes NF and Jackson, SP. (2000). A role for Saccharomyces cerevisiae histone H2A in DNA repair. Nature, 408: 1001-1004.
20. de la Torre-Ruiz MA and Lowndes NF. (2000). DUN1 defines one branch downstream of RAD53 for transcription and DNA damage repair in Sacharomyces cerevisiae. FEBS Letts, 485: 205-206.
19 R. Lowndes NF and Murguia, JR. (2000) Sensing and responding to DNA damage. Curr. Opin. Genet. & Dev. 10: 17-25.
18. de la Torre-Ruiz MA and Lowndes NF. (2000) The S. cerevisiae DNA damage checkpoint is required for efficient repair of double strand breaks by non-homologous end joining. FEBS Letts 467: 311-315.
17. GreenCM, Erdjument-BromageH, TempstP and Lowndes NF. (2000) A Novel Rad24 checkpoint Protein complex closely related to Replication Factor C. Curr. Biol. 10: 39-42.
16. Soulier J and Lowndes NF. (1999) The BRCT domain of the S. cerevisiae Rad9 checkpoint protein mediates Rad9/Rad9 interaction after DNA damage. Curr. Biol. 9: 551-554.
15 R. Lowndes NF. (1999). DNA damage-dependent checkpoints in yeasts and human cells. Eur J. Cancer 35: 1573-1574.
14. Vialard JE, Gilbert CS, Green, CM and Lowndes NF. (1998). The budding yeast Rad9 checkpoint protein is subjected to Mec1/Tel1-dependent hyperphosphorylation and interacts with Rad53 after DNA damage. EMBO J. 17: 5679-5688.
13. Freire R, Murguia JR, Tarsounas M, Lowndes NF, Moens PB and Jackson, SP. (1998). Human and mouse homologues of S. pombe rad1+ and S. cerevisiae RAD17: linkage to checkpoint control and mammalian meiosis. Genes & Dev.; 12: 2560-2573.
12. de la Torre-Ruiz, MA, Green CM and Lowndes NF. (1998) RAD9 and RAD24 define two additive, interacting branches of the DNA damage checkpoint pathway in budding yeast normally required for Rad53 modification and activation. EMBO J, 17: 2687-2698.
11. Aboussekhra A., Vialard JE, Morrison DE, de la Torre-Ruiz MA, Cernakova, L., Fabre, F and Lowndes, NF (1996). The RAD9 checkpoint gene of Saccharomyces cerevisiae controls a DNA damage-specific transcriptional response. EMBO J. 15: 3912-3922.
10 R. Merrill G, Morgan B, Lowndes NF and Johnston LH (1992). Periodic transcription during the late G1 phase of the budding yeast cell cycle. BioEssays, 14: 823-830.
9. Lowndes NF, Johnson AL, Breeden L and Johnston LH. (1992) SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast. Nature, 357:505-508.
8 R. Johnston LH, Lowndes NF, Johnson AL and Sugino A. (1991) A cell-cycle-regulated trans-factor, DSC1, controls expression of DNA synthesis genes in yeast. Cold Spring Harb Symp Quant Biol. 56:169-176.
7. Johnston LH and Lowndes NF. (1992) Cell cycle control of DNA synthesis in budding yeast. Nucleic Acids Res. 20(10): 2403-2410.
6 R. Lowndes, N.F. and Johnston, L.H. (1992). Parallel pathways of cell cycle-regulated gene expression. Tr. Genet. 8: 79-81.
5. Lowndes NF, McInerny CJ, Johnson AL, Fantes PA, Johnston LH. (1992) Control of DNA synthesis genes in fission yeast by the cell-cycle gene cdc10+. Nature, 355: 449-453.
4. Lowndes NF, Johnson AL, Johnston LH. (1991) Coordination of expression of DNA synthesis genes in budding yeast by a cell-cycle regulated trans factor. Nature, 350: 247-250.
3. White JH, Johnson AL, Lowndes NF, Johnston LH. (1991) The yeast DNA ligase gene CDC9 is controlled by six orientation specific upstream activating sequences that respond to cellular proliferation but which alone cannot mediate cell cycle regulation. Nucleic Acids Res, 19: 359-364.
2. Lowndes NF, Bushel P, Mendelsohn L, Wu J, Yen MY, Allan M. (1990) A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional read-through by a viral promoter. Mol. Cell. Biol., 10: 4990-4995.
1. Lowndes NF, Paul J, Wu J, Allan M. (1988) c-Ha-ras bidirectional promoter expressed in vitro: location and regulation. Mol. Cell. Biol., 9: 3758-3770.