Rachel O’Neill



University of Connecticut
Department of Molecular & Cell Biology
354 Mansfield Road, Unit 1131
Beach Hall 323A
Storrs, CT 06269-1131

Telephone: 860-486-6031
Fax: 860-486-1936

Visit Professor Rachel O’Neill’s Website.


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.

Selected Publications:

Chin-Chi, C., Bowers, S., Lipinszki, Z., Palladino, J., Trusiak, S., Bettini, E., Rosin, L., Przewloka, M.R., Glover, D.M., O’Neill, R. J., Mellone, B.G. (2015) Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription. Developmental Cell doi:10.1016/j.devcel.2015.05.012.

Harris, S.E., Munshi-South, J., Obergfell, C., O’Neill, R.J. 2013. Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area. PLoS ONE 8(8): e74938. doi:10.1371/journal.pone.0074938.

Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KH, Copenhaver GP, Deluca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LE, Karpen G, Kops GJ, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O’Neill RJ, Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordeman L, Yanagida M, Yen TJ, Yoda K, Cleveland DW. 2013 Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res. 21(2):101-6. doi: 10.1007/s10577-013-9347-y.

Jue, N. K., Murphy, M. B., Kasowitz, S. D., Qureshi, S. M., Obergfell, C. J., Elsisi, S., Foley, R. J., O’Neill, R. J., O’Neill, M. J. 2013. Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach. BMC Genomics 14, 150.

Carone, D.M.  Zhang, C., Hall, L.E., C. Obergfell, B.R. Carone, M.J. O’Neill, R.J. O’Neill. 2013. Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading. Chromosome Research 21(1):49-62.DOI 10.1007/s10577-013-9337-0

Hall, L. E., Mitchell, S.E, and R. O’Neill. 2012. Pericentric and centromeric transcription: a perfect balance required. Chromosome Res 20(5):535-546.

O’Neill R. J. and Sullivan B. A. 2012. Foreword: the centromere and kinetochore in creatures great and small. Chromosome Res 20(5):461-463. (COVER)

Lindsay, J., Carone, D.M., J. Brown, L. Hall, S. Qureshi, S. Mitchell, N. Jannetty, G. Hannon, A. Pask, M. Renfree, M. O’Neill and R. O’Neill. 2012. Unique small RNA signatures uncovered in the tammar wallaby genome. BMC Genomics 13: 559: 10.1186/1471-2164-13-559.

Sharma, R.,  Goossens,B., Kun-Rodrigues, C., Teixeira, T., Othman, N.B., Bruford, M.W., Jue, N.K., Obergfell, C., O’Neill, R.J.,  Chikhi, L. 2012. Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One 7(11): e49533.

Yu H, Lindsay J, Feng ZP, Frankenberg S, Hu Y, Carone D, Shaw G, Pask AJ, O’Neill R, Papenfuss AT, Renfree MB. 2012. Evolution of coding and non-coding genes in HOX clusters of a marsupial. BMC Genomics. 2012 Jun 18;13(1):251.

Brown, J.B., S. Mitchell, and R.J. O’Neill. 2012. Making a long story short: noncoding RNAs and chromosome change. Heredity 108:42-49.

Brown, J.D., V. Piccuillo, and R. J. O’Neill. 2012. Retroelement Demethylation Associated with Abnormal Placentation in Mus musculus × Mus caroli Hybrids. Biology of Reproduction 86 (3) 88: 1-10.

Renfree et al, R. O’Neill co-senior author [Genome Assembly Team, senior author, Small RNA Analysis Team, Repeat Analysis team, senior author 2011. Genome biology of an Australian Marsupial. Genome Biology 12: R81.

Ferreri, G., J. Brown, N. Jue, C. Obergfell, C. Finn, M.J. O’Neill and R.J. O’Neill. 2011. Recent amplification of an endogenous retrovirus limited to the centromere. Journal of Virology 85(10): 4761-71.

Brown, J.D.,Carone, D.M., C. Finn, and R. J. O’Neill 2011. Centromere conversion and retention in somatic cell hybrids. Cytogenetics and Genome Research 134: 182-90.

Heider, T., Lindsay, J., Wang, C., O’Neill, R. J. & Pask, A. 2011. Enhancing genome assemblies by integrating non-sequence data. BMC Proc 5 supp 2, S7.

Longo, M. S., O’Neill, M. J. & O’Neill, R. J. 2011. Abundant human DNA contamination identified in non-primate genome databases. PLoS One 6(2): e16410.

O’Neill, R.J. and J. Brown. 2010. Chromosomes, Conflict and Epigenetics: chromosomal speciation revisited. Annual Reviews in Genomics and Human Genetics 11: 291-316.

Carone, D.M. and R.J.O’Neill. 2010. Marsupial Centomeres and Telomeres: Dynamic Chromosome Domains in Marsupial Genetics and Genomics.

Mlynarski, E.E., C.J. Obergfell, M.J. O’Neill, R.J. O’Neill. 2010 Divergent patterns of breakpoint reuse in Muroid rodents. Mammalian Genome 21(1-2):77-87. Epub 2009 Dec 22.

Mlynarski, E.E., C.J. Obergfell, M.J. O’Neill, R.J. O’Neill. 2010. A unique late-replicating XY to autosome translocation in Peromyscus melanophrys. Chromosome Research 18: 179-189.

Brown, J.D. and O’Neill, R. J. The mysteries of chromosome evolution in gibbons: methylation is a prime suspect. PLoS Genet 2009 June; 5(6).

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.

Carone, D.M., M.S. Longo, G.C. Ferreri, L.Hall, Kira V. Bulazel, M.J. O’Neill and R.J. O’Neill. 2009. A novel class of retroviral and satellite encoded small RNAs emanate from mammalian centromeres. Chromosoma 118: 113-125.

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.

Lawton, B.R. B.  R Carone, C. Obergfell, G. Ferreri, C. Gondolphi, J. L. VandeBerg, I. Imumorin, R. J. O’Neill, and M. J. O’Neill. 2008. Genomic Imprinting of IGF2 in Marsupials is Methylation Dependent. BMC Genomics 9: 205.

Mlynarski, E.E., C. Ramsdell, 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. Cytogenetics and Genome Research 121: 288-292.

Ramsdell, C., Glenn, J.W., R. J. O’Neill and M. Dewey. 2008. Peromyscus linkage map closely resembles Rattus BMC Evolutionary Biology 26(8): 65.

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 (3): 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 (4): 2507-17

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. Brownand 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. ONeill, 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 SRYMolecular 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.