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The Boddy Laboratory

Publications

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Nie, M., Moser, B.A., Nakamura, T.M., Boddy, M.N.  SUMO-targeted ubiquitin ligase activity can either suppress or promote genome instability, depending on the nature of the DNA lesion. PLoS Genet.  2017;13(5):e1006776. F1000Prime-Special Significance http://f1000.com/prime/727586562?bd=197173

Nie, M., and Boddy, MN. (2016) Cooperativity of the SUMO and Ubiquitin Pathways in Genome Stability.  Biomolecules. Feb 25;6(1):14.

Zilio, N., and Boddy, MN.  Improved tandem affinity purification tag and methods for isolation of proteins and protein complexes. Cold Spring Harb. Protoc.  2017;2017(3):pdb prot091611.

Nie, M., and Boddy, MN.  Large scale purification of sumoylated proteins from S. pombe. Cold Spring Harb. Protoc. 2017;2017(3):pdb prot091603.

Nie, M., Arner, E., Prudden, J., Schaffer, L., Boddy, M.N. Functional Crosstalk between the PP2A and SUMO Pathways Revealed by Analysis of STUbL Suppressor, razor 1-1.  PLoS Genetics. 2016; 12(7):e1006165.

Nie, M., Vashisht, AA, Wohlschlegel, JA, Boddy, MN (2015) High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification. Sci Rep. Sep 25;5:14389.

Nie, M., and Boddy, MN. (2015) Pli1 (PlAS1) SUMO Ligase Protected by the Nuclear Pore Associated SUMO Protease Ulp1 (SENP1/2). J. Biol. Chem. doi:10.1074/jbc.M115.673038.

Zilio N., Codlin S., Vashisht AA., Bitton DA., Head SR., Wohlschlegel JA., Bähler J., Boddy MN.   A Novel HDAC Complex in the Control of Transcription and Genome Stability.  Mol Cell Biol. 2014 Jul 7. pii: MCB.00519-14.

Groocock LM., Nie M., Prudden J., Moiani D., Wang T., Cheltsov A., Rambo RP., Arvai AS., Hitomi C., Tainer JA., Luger K., Perry JJ., Denchi-EL., Boddy MN. (2014) RNF4 interacts with both SUMO and nucleosomes to promote the DNA Damage Response.  EMBO Rep. 15(5):601-608.

Zilio, N., Wehrkamp-Richter, S., Boddy, MN. A new versatile system for rapid control of gene expression in the fission yeast Schizosaccharomyces pombe.  Yeast 29(10):425-434, 2012.

Wehrkamp-Richter, S., Hyppa, RW., Prudden, J., Smith, GR., Boddy MN. Meiotic DNA joint molecule resolution depends on Nse5-Nse6 of the Smc5-Smc6 holocomplex. Nucleic acids research. 40(19):9633-9646, 2012.

Nie, M., Aslanian, A., Prudden, J., Heideker, J., Vashisht, AA., Wohlschlegel, JA., Yates, JR., Boddy MN. Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 by SUMO and ubiquitin in STUbL-mediated genome stability functions. J Biol Chem. 287(35):29610-29619, 2012.

Groocock, LM., Prudden, J., Perry, JJ., Boddy MN. The RecQ4 orthologue Hrq1 is critical for DNA interstrand cross-link repair and genome stability in fission yeast. Mol Cell Biol. 32(2):276-87, 2012.

Prudden, J., Perry, J.J.P., Nie, M., Vashisht, A.A., Arvai, A.S., Hitomi, C., Guenther, G., Wohlschlegel, J.A., Tainer, J.A., Boddy, M.N. DNA Repair and Global Sumoylation are Regulated by Distinct Ubc9 Non-covalent Complexes Mol. Cell. Biol. 11:2299-310, 2011.

Heideker, J., Prudden, J., Perry, J.J.P., Tainer, J.A., Boddy, M.N. SUMO-targeted Ubiquitin Ligase, Rad60 and Nse2 SUMO Ligase Suppress Spontaneous Top1-mediated DNA damage and Genome Instability. PLoS Genetics epub1001320, 2011 

Bekes, M., Prudden, J., Srikumar, T., Raught, B., Boddy, M.N., Salvesen, G.S. The dynamics and mechanism of sumo chain deconjugation by SUMO-specific proteases. J. Biol. Chem. (Epub ahead of print), 2011. 

Prudden, J., Perry, J.J., Arvai, A.S., Tainer, J.A., Boddy, M.N. Molecular mimicry of SUMO promotes DNA repair. Nat. Struct. Mol. Biol. 16:509, 2009. (News & Views) (Faculty 1000)

Heideker, J., Perry, J.J., Boddy, M.N. Genome stability roles of SUMO-targeted ubiquitin ligases. DNA Repair (Amst) 8:517, 2009.

Perry, J.J., Tainer, J.A., Boddy, M.N. A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem. Sci. 33:201, 2008.

Pebernard, S., Schaffer, L., Campbell, D., Head, S.R., Boddy, M.N. Localization of Smc5/6 to centromeres and telomeres requires heterochromatin and SUMO, respectively. EMBO J. 27:3011, 2008.

Pebernard, S., Perry, J.J., Tainer, J.A., Boddy, M.N. Nse1 RING-like domain supports functions of the Smc5-Smc6 holocomplex in genome stability. Mol. Biol. Cell 19:4099, 2008.

Prudden, J., Pebernard, S., Raffa, G., Slavin, D.A., Perry, J.J., Tainer, J.A., McGowan, C.H., Boddy, M.N. SUMO-targeted ubiquitin ligases in genome stability. EMBO J. 26:4089, 2007. (News & Views) (Faculty 1000)

Raffa, G.D., Wohlschlegel, J., Yates, J.R., 3rd, Boddy, M.N. SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association. J. Biol. Chem. 281:27973, 2006.

Pebernard, S., Wohlschlegel, J., McDonald, W.H., Yates, J.R., 3rd, Boddy, M.N. The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Mol. Cell. Biol. 26:1617, 2006. (Faculty 1000)

Kai, M., Boddy, M.N., Russell, P., Wang, T.S. Replication checkpoint kinase Cds1 regulates Mus81 to preserve genome integrity during replication stress. Genes Dev. 19:919, 2005.

Pebernard, S., McDonald, W.H., Pavlova, Y., Yates, J.R., 3rd, Boddy, M.N. Nse1, Nse2, and a novel subunit of the Smc5-Smc6 complex, Nse3, play a crucial role in meiosis. Mol. Biol. Cell 15:4866, 2004.

Blais, V., Gao, H., Elwell, C.A., Boddy, M.N., Gaillard, P.H., Russell, P., McGowan, C.H. RNA interference inhibition of Mus81 reduces mitotic recombination in human cells. Mol. Biol. Cell 15:552, 2004.

Smith, G.R., Boddy, M.N., Shanahan, P., Russell, P. Fission yeast Mus81.Eme1 Holliday junction resolvase is required for meiotic crossing over but not for gene conversion. Genetics 165:2289, 2003.

McDonald, W.H., Pavlova, Y., Yates, J.R., 3rd, Boddy, M.N. Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex. J. Biol. Chem. 278:45460, 2003.

Boddy, M.N., Shanahan, P., McDonald, W.H., Lopez-Girona, A., Noguchi, E., Yates, I.J., Russell, P. Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Mol. Cell. Biol. 23:5939, 2003.

Tanaka, K., Boddy, M.N., Chen, X.B., McGowan, C.H., Russell, P. Threonine-11, phosphorylated by Rad3 and atm in vitro, is required for activation of fission yeast checkpoint kinase Cds1. Mol. Cell. Biol. 21:3398, 2001.

Chen, X.B., Melchionna, R., Denis, C.M., Gaillard, P.H., Blasina, A., Van de Weyer, I., Boddy, M.N., Russell, P., Vialard, J., McGowan, C.H. Human Mus81-associated endonuclease cleaves Holliday junctions in vitro. Mol. Cell 8:1117, 2001.

Boddy, M.N., Russell, P. DNA replication checkpoint. Curr. Biol. 11:R953, 2001.

Boddy, M.N., Gaillard, P.H., McDonald, W.H., Shanahan, P., Yates, J.R., 3rd, Russell, P. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell 107:537, 2001. (Faculty 1000)

Rhind, N., Baber-Furnari, B.A., Lopez-Girona, A., Boddy, M.N., Brondello, J.M., Moser, B., Shanahan, P., Blasina, A., McGowan, C., Russell, P. DNA damage checkpoint control of mitosis in fission yeast. Cold Spring Harb. Symp. Quant. Biol. 65:353, 2000.

Boddy, M.N., Lopez-Girona, A., Shanahan, P., Interthal, H., Heyer, W.D., Russell, P. Damage tolerance protein Mus81 associates with the FHA1 domain of checkpoint kinase Cds1. Mol. Cell. Biol. 20:8758, 2000.

Baber-Furnari, B.A., Rhind, N., Boddy, M.N., Shanahan, P., Lopez-Girona, A., Russell, P. Regulation of mitotic inhibitor Mik1 helps to enforce the DNA damage checkpoint. Mol. Biol. Cell 11:1, 2000.

Duprez, E., Saurin, A.J., Desterro, J.M., Lallemand-Breitenbach, V., Howe, K., Boddy, M.N., Solomon, E., de The, H., Hay, R.T., Freemont, P.S. SUMO-1 modification of the acute promyelocytic leukaemia protein PML: implications for nuclear localisation. J. Cell Sci. 112 ( Pt 3):381, 1999.

Brondello, J.M., Boddy, M.N., Furnari, B., Russell, P. Basis for the checkpoint signal specificity that regulates Chk1 and Cds1 protein kinases. Mol. Cell. Biol. 19:4262, 1999.

Boddy, M.N., Russell, P. DNA replication checkpoint control. Front. Biosci. 4:D841, 1999.

Howe, K., Williamson, J., Boddy, N., Sheer, D., Freemont, P., Solomon, E. The ubiquitin-homology gene PIC1: characterization of mouse (Pic1) and human (UBL1) genes and pseudogenes. Genomics 47:92, 1998.

Boddy, M.N., Furnari, B., Mondesert, O., Russell, P. Replication checkpoint enforced by kinases Cds1 and Chk1. Science 280:909, 1998.

Boddy, M.N., Duprez, E., Borden, K.L., Freemont, P.S. Surface residue mutations of the PML RING finger domain alter the formation of nuclear matrix-associated PML bodies. J. Cell Sci. 110 ( Pt 18):2197, 1997.

Saurin, A.J., Borden, K.L., Boddy, M.N., Freemont, P.S. Does this have a familiar RING? Trends Biochem. Sci. 21:208, 1996.

Boddy, M.N., Howe, K., Etkin, L.D., Solomon, E., Freemont, P.S. PIC 1, a novel ubiquitin-like protein which interacts with the PML component of a multiprotein complex that is disrupted in acute promyelocytic leukaemia. Oncogene 13:971, 1996.

Otto, W.R., Nanchahal, J., Lu, Q.L., Boddy, N., Dover, R. Survival of allogeneic cells in cultured organotypic skin grafts. Plast. Reconstr. Surg. 96:166, 1995.

Borden, K.L., Boddy, M.N., Lally, J., O'Reilly, N.J., Martin, S., Howe, K., Solomon, E., Freemont, P.S. The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML. EMBO J. 14:1532, 1995.

Boddy, M.N., Freemont, P.S., Borden, K.L. The p53-associated protein MDM2 contains a newly characterized zinc-binding domain called the RING finger. Trends Biochem. Sci. 19:198, 1994.