Professor Rachel J. O'Neill
Education: Ph.D. La Trobe University.
Research Interests: My lab uses molecular genetic and cytogenetic techniques to study centromere determinance; centromere function and evolution; small RNA biogenesis; transcriptional control of chromatin modifiers; chromosome evolution; speciation and hybrid dysgenesis in several model systems, including human, mouse, marsupial, platypus (somatic cells, germ cells and embryonic stem cells). Using techniques such as in situ hybridization, microarray screening, cell assays, artificial chromosome constuction, and next-generation sequencing platforms (Illumina and 454 pyrosequencing), we are addressing the hypothesis that small RNA forms mediate centromere function.
We are also using these techniques to study species-specific placental development and evolution with respect to retroelement load; transposable elements and retroviruses; and, the epigenetic effectors of gene expression and chromosome structure in models as diverse as deer mice and matrotrophic fish.
Brown J.D. and R.J. O'Neill. 2009. The Mysteries of Chromosome Evolution in Gibbons: Methylation Is a Prime Suspect. PLoS Genet 5(6): e1000501. doi:10.1371/journal.pgen.1000501
O'Neill, R.J. and D.M. Carone. 2009. Chapter 4: The role of ncRNA in centromeres: lessons from marsupials. in: Centromere: structure and evolution ed: D. Ugarkovic, Springer Press. Pp77-101.
Longo, M.S., Carone, D.M., Marzelli, M., M.J. O'Neill, E. Green, NISC Sequencing Consortium, R.J. O'Neill. 2009. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10:334 (24 July 2009)
Mlynarski, E.E., C. Ramsdell, M.J. Dewey, C. Obergfell, W. Rens, M. J. O'Neill and R.J. O'Neill. 2008. Peromyscus maniculatus and Mus musculus Synteny Map Established by Reciprocal Chromosome Painting. In Press Cytogenetic and Genome Research
Ramsdell, C., Glenn, J.W., R. J. O'Neill and M. Dewey. 2008. Peromyscus linkage map closely resembles Rattus. In Press BMC Evolutionary Biology
Brown, J.D., D. Golden, R.J.O'Neill. 2008. Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 91: 267-273.
Metcalfe, C.J., K.V. Bulazel, G. C. Ferreri, W. Rens, E. Schroeder-Reiter, G. Wanner, M. D. B. Eldridge, and R. J. O'Neill. 2007. Genomic instability within centromeres of interspecific marsupial hybrids. Genetics 177: 2507-2517.
O'Neill, M.J., B. R. Lawton, M. Mateos, D. M. Liscinsky, G. C. Ferreri, T. Hrbek, D. N. Reznick and R. J. O'Neill. 2007. Ancient and Continuing Darwinian Selection on IGF2 in Placental Fishes. PNAS (COVER) 104: 12404-9.
Bulazel, K.V., G. C. Ferreri, M. D. B. Eldridge and R. J. O'Neill. 2007. Species-specific shifts in centromere sequence composition are coincident with break point reuse in karyotypically divergent lineages. Genome Biology 8(8):R170.
Duselis, A. R. C. Obergfell, J.A. Mack, M. J. O'Neill, Q. K. Nguyen, R. J. O'Neill and P. B. Vrana. 2007. Cell-Cycle and extra-cellular matrix gene expression changes during deer mouse (Peromyscus) hybrid placental development. Reproduction Fertility and Development 19: 1-14.
Smilowitz, H.M. J. Weissenberger, J. Weis, R. J. O'Neill, J. Brown and J.A. Laissue. 2007. A Transplantable Mouse Tumor Model for Malignant Gliomas. J. Neurosurgery 106(4):652-9.
Ambrosi, D.J., B. Tanasijevic, A. Kaur, C. Obergfell, R.J. O'Neill, W. Krueger, and T.P. Rasmussen. 2007. Genome-wide Reprogramming in Hybrids of Somatic Cells and Embryonic Stem Cells. Stem Cells 25: 1104-1113.
Kronforst, M.R., L.G.Yound, C. McNeely, R.J. O'Neill, and L.E. Gilbert. 2006. Autosomal coupling of mate preference and preference cue in Heliconius butterflies. PNAS 103: 6575-6580.
Bulazel, K., Metcalfe, C., Ferreri, G.C., Yu, J., Eldridge, M.D.B. and R.J. O'Neill. 2006. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome. Genetics 172: 1129-1137.
Lawton, B.R., C. Obergfell, R.J. O'Neill, and M. J. O'Neill. 2006. Physical mapping of the IGF2 locus in the South American Opossum Monodelphis domestica. Cytogenetics and Genome Research 116: 130-1.
Ford, K.K., J.A. Mack and R.J. O'Neill. 2005. Multiple independent pseudogene derviations indicate increased instability of the mdm2 locus in Mus caroli. Molecular Biology Reports 32:95-101.
Lawton, B.R., L. Sevigny, C. Obergfell, D. Reznick, and R.J. O'Neill, O'Neill, M.J. 2005. Allelic Expression Profile of IGF2 in Live-bearing, Matrotrophic Fishes. Development, Genes and Evolution 215(4):207-12.
Liscinsky, D, Ferreri, G. C.,Mack, J. M.D.B. Eldridge and R.J. O'Neill. 2005. Retention of latent centromeres in the mammalian genome. Journal of Heredity 96: 217-224.
Ferreri, G. C, M. Marzelli, W. Rens, and R.J. O'Neill. 2004. Centromere specific retroviral element associated with breaks of synteny in macropodine marsupials. Cytogenetic and Genome Research 107: 115-118.
Carvalho-Silva, D.R., R.J. O'Neill, J. D. Brown, K. Huynh, P. D. Waters, A. J. Pask, M. L. Delbridge and J. A. M. Graves. 2004. Molecular characterization and evolution of X and Y-borne ATRX homologues in American marsupials. Chromosome Research 12: 795-804.
O'Neill, R.J., G.C. Ferreri, and M.J. O'Neill. 2004. Elements and mechanisms of genome change. In Mammalian Genomics eds. A. Ruvinsky and J. Graves. CABI: Oxford
O'Neill, R.J., M.D.B. Eldridge, C.J. Metcalfe. 2004. Centromere dynamics and chromosome evolution in marsupials. J. Heredity 95: 375-381. (COVER)
Qu, H., R.J. Waugh O'Neill, and M. Wei. 2004 The effect of cell behavior on apatites with different fluorine contents. Key Engineering Materials 284-286: 577-580.
Wilder J.A., E.G. Dyreson, R.J. O'Neill, M.L. Spangler, R. Gupta, A.S. Wilder, and H. Hollocher 2004. Contrasting modes of natural selection acting on pigmentation genes in the Drosophila dunni subgroup.J Exp Zoolog B Mol Dev Evol. 15;302(5):469-82.
Brown, J.D., M. Strbuncelj, C. Giardina and R.J.W. O'Neill. 2003. Interspecific hybridization induced amplification of mdm2 on double minutes in a Mus hybrid. Cytogenet Genome Res 98:184-88.
Pask, A.J., J.L. Harry, J.A.M. Graves, R.J. Waugh O'Neill, S.L.Layfield, G. Shaw and M.B. Renfree. 2002. SOX9 has both conserved and novel roles in marsupial sexual differentiation. Genesis 33: 131-9.
Wilder, J.A., T. Diaz, R.J. O'Neill, J. Kenney, and H. Hollocher. 2002. Characterization and isolation of novel microsatellites from the Drosophila dunni subgroup. Genet Res 80:177-85.
O'Neill, R. J. W., M. D. B. Eldridge, and J.A.M Graves. 2001. Chromosome heterozygosity and de novo chromosome rearrangements in mammalian interspecific hybrids. Mammalian Genome 12: 256-259.
Hollocher, H., K. Agopian, J. Waterbury, R.W. O'Neill, A. W. Davis. 2000. Characterization of defects in adult germline development and oogenesis of sterile and rescued female hybrids in crosses between Drosophila simulans and Drosophila melanogaster. J. Exp Zoology (Mol and Dev Evol) 228: 205-218.
O'Neill, M.J. and R.J. O'Neill. 1999. Whatever happened to SRY? Cellular and Molecular Life Sciences. 56: 883-893.
O'Neill, R.J.Waugh, M.J. O'Neill and J.A.M. Graves. 1999. Genome evolution: Role of methylation in eutherian hybrids. Nature 401: 131-132.
Martin, J., E. Herniou, J. Cook, R.J.Waugh O'Neill, and M. Tristem. 1999. Inter-class transmission and phyletic host tracking in murine leukaemia-related retroviruses. J. Virology 73: 2442-9.
O'Neill, R.J.Waugh, M.D.B. Eldridge, M.A. Ferguson-Smith, P.C. O’Brien, J.A.M. Graves. 1999. Chromosome evolution in kangaroos (Marsupialia: Macopodidae): Cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n=22 ancestral karyotype. Genome 42: 525-530.
Toder, R., R.J.Waugh O'Neill and J.A.M. Graves. 1999. Chromosome painting in marsupials. ILAR Journal 39(2,3): 92-95.
O'Neill, R.J.Waugh, M.J. O'Neill and J.A.M. Graves. 1998. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature 393: 68-72.
O'Neill, R.J.Waugh, F.Brennan, M.L. Delbridge, and J.A.M. Graves. 1998. De novo insertion of an intron into the mammalian sex determining gene, SRY. Proceedings of the National Academy of SciencesUSA 95:1653-1657.
O'Neill, R.J.Waugh, M.D.B. Eldridge, R.H. Crozier, and J.A.M. Graves. 1997. Low levels of sequence divergence in Rock Wallabies (Petrogale) suggest a lack of positive directional selection in SRY. Molecular Biology and Evolution 14(3): 350-353.
Martin, J., E. Herniou, J. Cook, R.J.Waugh O'Neill, and M. Tristem. 1997. Human endogenous retrovirus type-I related viruses have an apparently widespread distribution within vertebrates. Journal of Virology 71(1) 437-443.
Graves, J.A.M., S.I. Cook, R.J.Waugh O'Neill, R. Glass, A. Pask, and M.L. Delbridge. 1997. Biological control of possums. Proceedings of the New Zealand Royal Society (misc series 45) 62-72.
Watson, C.M., P.G. Johnston, K.A. Rodger, L.M. McKenzie, R.J. Waugh O'Neill, and D.W. Cooper. 1997. Sex chromosome complements and Sry status of two intersexual marsupials and one abnormal marsupial. Reproduction, Fertility and Development 9(2): 233-241.
Graves, J.A.M. and R.J.Waugh O'Neill. 1997. Sex chromosomes and Haldane’s Rule. Journal of Heredity 88(5): 358-360.
Toder, R., R.J.Waugh O'Neill, J. Wienberg, L. Voillaire and J.A.M. Graves. 1997. Comparative chromosome painting between two marsupial species: origins of an XX/XY1Y2 sex chromosome system. Mammalian Genome 8(6): 418-422.
Delbridge, M.L., J.L. Harry, R.J.Waugh O'Neill, R. Toder, K. Ma, A.C. Chandley, and J.A.M. Graves. 1996. A human candidate spermatogenesis gene RBM1 is conserved and amplified on the marsupial Y chromosome. Nature Genetics 15(2): 131-136.
Pamilo, P. and R.J.Waugh O'Neill. 1996. Evolution of the Sry genes. Molecular Biology and Evolution 14(1): 49-55.