Rachel O'Neill

Board of Trustees Distinguished Professor

Molecular and Cell Biology / Genetics and Genomics

Education: PhD La Trobe University

Research Interests:  For most eukaryotic species, over 50% of the genome consists of repetitive elements, yet we lack a fundamental understanding of their impact on genome stability during dynamic processes such as cell division, viral invasion, tumorigenesis, and development.

My research programs employ molecular genetics, genomics and computational approaches to study the mechanisms that maintain, and disrupt, genome stability with a particular focus on repetitive elements. Projects include studying: retroelement transcription and centromere function; novel small RNA biogenesis pathways; and global chromosome and genome changes during instability (such as in cancer and hybrid dysgenesis). In addition, we use a diverse set of rapidly evolving next generation sequencing (NGS) technologies and novel library preparation and computational methodologies for drafting and characterizing genome sequences in efforts to establish broad eukaryotic species as models for studying genome biology. Recently, we have expanded our efforts towards applying broad NGS techniques to both model and non-model systems to understand the dynamic response of the genome to environmental queues, such as global warming.

Select Recent Publications – see: https://roneill.lab.uconn.edu/publications/ for full list

1. Harris A. Lewin, Stephen Richards and The Earth Biogenome Project Working Group (R. O’Neill, Member): 2021. The Earth BioGenome Project 2020: Starting the Clock. Cell Genomics in press
2. Hartley, G., Ohkavat, M., Carbone, L., O’Neill, R. J. (Co last authors). 2021. Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition. Molecular Biology and Evolution msab148, https://doi.org/10.1093/molbev/msab148
3. Ahmad, S.F.; Jehangir, M.; Cardoso, A.L.; Wolf, I.R.; Margarido, V.P.; Cabral-de-Mello, D.C.; O’Neill, R.; Valente, G.T.; Martins, C. B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes. BMC Genomics 2020, 21, 656, doi:10.1186/s12864-020-07072-1.
4. Mariam Okhovat, M., Nevonen, K.A., Davis, B., Michener, P., Ward, S., Milhaven, M., Harshman, L., Sohota, A., O’Neill, R.J., Ahituv, N., Veeramah, K.R., and Carbone, L. Co-option of the gibbon-specific LAVA retrotransposon in DNA repair pathways. PNAS 117 (32) 19328-19338.
5. O’Neill, R.J., 2020. Seq’ing identity and function in a repeat-derived noncoding RNA world. Chromosome Research 28, 111–127.
6. Deakin, J., and O’Neill, R.J. 2019. Evolution of Marsupial Genomes. Annual Review of Animal Biosciences vol 8.
7. Deakin, J. , Potter,, O’Neill, R.J., Ruiz-Herrera, A., Cioffi, M., Eldridge, M., Fukui, K., Graves, J.M., Griffin, D., Grutzner, F., Kratochvíl, L., IMiura, I., Rovatsos, M., Srikulnath, K., Wapstra, E., Ezaz, T., 2019. Chromosomics: bridging the gap between genomes and chromosomes. Genes 10 (8), 627.
8. Hartley, G., & O’Neill, R. J. 2019. Centromere Repeats: Hidden Gems of the Genome. Genes, (3 ed., vol. 10). 10.3390/genes10030223.
9. Smalec, B. M., Heider, T.N., Flynn, B.L., and O’Neill, R.J. A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Research. doi.org/10.1007/s10577-019-09605-1
10. Cilhoroz, B; Schifano, E; Ash, G; Panza, Gr; Lamberti, L; Chen, M-H; Deshpande, V; Zaleski, A; Farinatti, P ; Santos, Lu; Taylor, Beth; O’Neill, R; Thompson, P; Pescatello, L. 2018. Furin variant associations with postexercise hypotension are intensity and race dependent. Physiological Reports 274. 10.1249/01.mss.0000535988.19797.e9.
11. Brown, J. D., Crivello, J., and O’Neill, R. J. 2018. An Updated Genetic Map of Peromyscus with Chromosomal Assignment of Linkage Groups. Mammalian Genome 29:5–6, pp344–352 (COVER)
12. Lazar, H., Nevonen, K.A., O’Connell, B., McCann, C., O’Neill, R.J., Green, R.E., Meyer, T.J., Okhovat, M., and L. Carbone 2018. Epigenetic maintenance of topological domains in the highly rearranged gibbon genome. Genome Research. 28(7):983-997, doi:10.1101/gr.233874.117
13. Johnson, R. ,O’Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Yuanyuan Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O’Neill, R.J., Colgan, D.C., Russell, T.L., Alquezar-Planas, D.A., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y., Deakin, J.E., Di Palma, F., Duda, Z., Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N., Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K. 2018. Adaptation and conservation insights from the koala genome. Nature Genetics 50, 1102–1111 h (COVER) https://doi.org/10.1038/s41588-018-0153-5.
14. Jue, N., Foley, R., Reznick, D., O’Neill, R.J. and O’Neill, M.J. 2018. Tissue-specific transcriptome for Poeciliopsis prolifica reveals evidence for genetic adaptation related to the evolution of a placental fish. G3: Genes|Genomes|Genetics 8(7):2181-2192; 10.1534/g3.118.200270.
15. Yang Y., Gu, , Sasaki, T., Crivello, J., O’Neill, R.J., Gilbert, D. and J. Ma. 2018. Continuous-trait probabilistic model for comparing multi-species functional genomic data. Cell Systems 7(2): 208-218.e11. doi: 10.1016/j.cels.2018.05.022.
16. Klein, S.J. and O’Neill, R. J. 2018. Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Research. Volume 26, Issue1–2, pp 5–23 https://doi.org/10.1007/s10577-017-9569-5 (COVER)
17. Bucklin, , Questel, J.M., DiVito, K., Smolina, I., Choquet, M., Hoarau, G. and O’Neill, R.J. 2018. Population Genomics of Marine Zooplankton; Chapter 19 in: Population Genomics: Marine Organisms, Editors: Om P. Rajora and Marjorie Oleksiak
18. Feigin, C., Axel, Y., Newton, H., Schmitz, J., Doronina, L., Hipsley, C.A., Mitchell, K.J., Gower, G., Llamas, B., Soubrier, J., Heider, T.N., Menzies, B.R., Cooper, A., O’Neill, R.J. and Pask, A.J. 2018. Genome of the Tasmanian Tiger Provides Insights into the Evolution and Demography of an Extinct Marsupial. Nature Ecology and Evolution 2:182–192; DOI:10.1038/s41559-017-0417-y
19. Johnson, W., Yewdell, W.T., Bell, J.C., McNutty, S.M., Duda, Z., O’Neill, R.J., Sullivan, B.A., and Straight, A. 2017. RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife. 6:e25299 DOI: 10.7554/eLife.25299
20. Jue N.K. Batta-Lona, P.G., Trusiak S, Obergfell C, Bucklin A, O’Neill MJ, O’Neill R.J. 2016. Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea). Genome Biol Evol. Oct 30;8(10):3171-3186. PubMed PMID: 27624472; PubMed Central PMCID: PMC5174732.