Rachel J O'Neill

Summary

Affiliation: University of Connecticut
Country: USA

Publications

  1. ncbi request reprint Transcriptional profiles of bovine in vivo pre-implantation development
    Zongliang Jiang
    Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
    BMC Genomics 15:756. 2014
  2. pmc Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach
    Nathaniel K Jue
    Department of Molecular and Cell Biology, University of Connecticut, 354 Mansfield Road, Storrs, CT 06235, USA
    BMC Genomics 14:150. 2013
  3. pmc Abundant human DNA contamination identified in non-primate genome databases
    Mark S Longo
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 6:e16410. 2011
  4. pmc Evolution of coding and non-coding genes in HOX clusters of a marsupial
    Hongshi Yu
    ARC Centre of Excellence in Kangaroo Genomics, The University of Melbourne, Melbourne, Victoria 3010, Australia
    BMC Genomics 13:251. 2012
  5. pmc Unique small RNA signatures uncovered in the tammar wallaby genome
    James Lindsay
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    BMC Genomics 13:559. 2012
  6. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
  7. pmc Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages
    Kira V Bulazel
    Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
    Genome Biol 8:R170. 2007
  8. pmc Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)
    Clifton M Ramsdell
    Department of Genetics and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    BMC Evol Biol 8:65. 2008
  9. ncbi request reprint The role of ncRNA in centromeres: a lesson from marsupials
    Rachel J O'Neill
    Center for Applied Genetics and Technology, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Prog Mol Subcell Biol 48:77-101. 2009
  10. ncbi request reprint A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres
    Dawn M Carone
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Chromosoma 118:113-25. 2009

Collaborators

  • MICHAEL J O'NEILL
  • Betty R Lawton
  • Mark S Longo
  • Robert W Meredith
  • Jingwei Yu
  • Willem Rens
  • Chenwei Wang
  • Mariana Mateos
  • Tomas Hrbek
  • D Reznick
  • Andrew J Pask
  • Dawn M Carone
  • Craig Obergfell
  • Gianni C Ferreri
  • James Lindsay
  • Judith D Brown
  • Kira V Bulazel
  • Laura E Hall
  • Hongshi Yu
  • Marilyn B Renfree
  • Mark D B Eldridge
  • Zongliang Jiang
  • Nathaniel K Jue
  • Sarah E Mitchell
  • Anthony T Papenfuss
  • Geoff Shaw
  • Yanqiu Hu
  • Zhi Ping Feng
  • Thomas N Heider
  • Benjamin R Carone
  • Laura Hall
  • Elisabeth E Mlynarski
  • Michael J Dewey
  • Clifton M Ramsdell
  • Cushla J Metcalfe
  • Kira Bulazel
  • Yong Tang
  • Yijun Ruan
  • Jinbo Bi
  • Jingbo Chen
  • Jiangwen Sun
  • Xiuchun Cindy Tian
  • Hong Dong
  • Xinbao Zheng
  • Oscar Luo
  • Craig J Obergfell
  • Sohaib M Qureshi
  • Seth D Kasowitz
  • Robert J Foley
  • Chu Zhang
  • Michael B Murphy
  • Sahar Elsisi
  • Greg Hannon
  • Stephen Frankenberg
  • Judy Brown
  • Dawn Carone
  • Nicholas Jannetty
  • Vanessa Piccuillo
  • Sohaib Qureshi
  • Marilyn Renfree
  • Yoshiyuki Sakaki
  • Daniel Thomas
  • Vandita Joshi
  • Danielle Hickford
  • Christie L Kovar
  • Sumio Sugano
  • Chyn Jing
  • Xing zhi Song
  • Sarah Williams
  • Mehlika Hazar-Rethinam
  • Jixin Deng
  • Nanette Y Schneider
  • Matthew J Wakefield
  • Richard A Gibbs
  • Thomas Heider
  • Javier Herrero
  • Joshua Y Shen
  • Amber Stephens
  • Shalini N Jhangiani
  • Jennifer A M Graves
  • Keng Yih Chew
  • Yutaka Suzuki
  • Yoko Kuroki
  • Shunsuke Suzuki
  • Annette McGrath
  • Elizabeth Kuczek
  • Kathryn Beal
  • John Davis
  • Margaret L Delbridge
  • Stephen M J Searle

Detail Information

Publications24

  1. ncbi request reprint Transcriptional profiles of bovine in vivo pre-implantation development
    Zongliang Jiang
    Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
    BMC Genomics 15:756. 2014
    ..The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology...
  2. pmc Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach
    Nathaniel K Jue
    Department of Molecular and Cell Biology, University of Connecticut, 354 Mansfield Road, Storrs, CT 06235, USA
    BMC Genomics 14:150. 2013
    ..However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals...
  3. pmc Abundant human DNA contamination identified in non-primate genome databases
    Mark S Longo
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 6:e16410. 2011
    ..We discuss issues this may raise as well as present data that gives insight as to how this may be occurring...
  4. pmc Evolution of coding and non-coding genes in HOX clusters of a marsupial
    Hongshi Yu
    ARC Centre of Excellence in Kangaroo Genomics, The University of Melbourne, Melbourne, Victoria 3010, Australia
    BMC Genomics 13:251. 2012
    ..The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals...
  5. pmc Unique small RNA signatures uncovered in the tammar wallaby genome
    James Lindsay
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    BMC Genomics 13:559. 2012
    ....
  6. pmc Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development
    Marilyn B Renfree
    The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
    Genome Biol 12:R81. 2011
    ..Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development...
  7. pmc Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages
    Kira V Bulazel
    Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
    Genome Biol 8:R170. 2007
    ....
  8. pmc Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)
    Clifton M Ramsdell
    Department of Genetics and the Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    BMC Evol Biol 8:65. 2008
    ..Nevertheless, early karyotypic analyses of the three groups suggest Peromyscus to be exhibit greater similarities with Rattus than with Mus...
  9. ncbi request reprint The role of ncRNA in centromeres: a lesson from marsupials
    Rachel J O'Neill
    Center for Applied Genetics and Technology, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Prog Mol Subcell Biol 48:77-101. 2009
    ..We highlight the current understanding of the wallaby centromere and the role of transcription in centromere function...
  10. ncbi request reprint A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres
    Dawn M Carone
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Chromosoma 118:113-25. 2009
    ..The discovery of this new RNA form brings together several independent lines of evidence that point to a conserved retroviral-encoded processed RNA entity within eukaryotic centromeres...
  11. pmc Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty
    Mark S Longo
    Center for Applied Genetics and Technology, Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    BMC Genomics 10:334. 2009
    ..Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined...
  12. pmc Genomic instability within centromeres of interspecific marsupial hybrids
    Cushla J Metcalfe
    Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269, USA
    Genetics 177:2507-17. 2007
    ..We discuss possible reasons and mechanisms for the centromeric instability and remodeling observed in all four macropodid hybrids...
  13. ncbi request reprint Hypermorphic expression of centromeric retroelement-encoded small RNAs impairs CENP-A loading
    Dawn M Carone
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Chromosome Res 21:49-62. 2013
    ..We propose that tight regulation of the processing of this new class of small RNAs, crasiRNAs, is an integral component of the epigenetic framework necessary for centromere establishment...
  14. pmc Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes
    MICHAEL J O'NEILL
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Proc Natl Acad Sci U S A 104:12404-9. 2007
    ..Our observations provide a rare example of natural selection acting in synchrony at the phenotypic and molecular level. These results also constitute the first direct evidence of parent-offspring conflict driving gene evolution...
  15. pmc Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere
    Gianni C Ferreri
    Department of Molecular and Cell Biology, University of Connecticut, 354 Mansfield Rd, U2131, Storrs, CT 06269, USA
    J Virol 85:4761-71. 2011
    ..rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events...
  16. pmc Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome
    Kira Bulazel
    Department of Molecular and Cell Biology, University of Connecticut, Storrs 06269, USA
    Genetics 172:1129-37. 2006
    ..rufogriseus...
  17. pmc Genomic imprinting of IGF2 in marsupials is methylation dependent
    Betty R Lawton
    Department of Molecular and Cell Biology, University of Connecticut, 354 Mansfield Rd, Storrs, CT 06269, USA
    BMC Genomics 9:205. 2008
    ....
  18. ncbi request reprint Retroelement demethylation associated with abnormal placentation in Mus musculus x Mus caroli hybrids
    Judith D Brown
    Diagnostic Genetic Sciences Program, Department of Allied Health Sciences, University of Connecticut, Storrs, Connecticut 06269 2131, USA
    Biol Reprod 86:88. 2012
    ..To our knowledge, the present data provide the first report of retroelement activation linked to decreased methylation in a eutherian hybrid system...
  19. ncbi request reprint Pericentric and centromeric transcription: a perfect balance required
    Laura E Hall
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Chromosome Res 20:535-46. 2012
    ..It is clear that maintaining a fine balance of transcriptional output is critical, as deviations from this balance result in centromere disfunction and genomic instability...
  20. ncbi request reprint A unique late-replicating XY to autosome translocation in Peromyscus melanophrys
    Elisabeth E Mlynarski
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269, USA
    Chromosome Res 18:179-89. 2010
    ..Thus, autosomal regions derived from translocations involving repeat-rich material may retain some epigenetic marks specific to the sex chromosomes despite loss of epigenetic silencing activity...
  21. ncbi request reprint Allelic expression of IGF2 in live-bearing, matrotrophic fishes
    Betty R Lawton
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Dev Genes Evol 215:207-12. 2005
    ..We found IGF2 to be expressed bi-allelically throughout embryonic development in both species...
  22. pmc Enhancing genome assemblies by integrating non-sequence based data
    Thomas N Heider
    Department of Molecular and Cellular Biology, University of Connecticut, 06269, Storrs CT, USA
    BMC Proc 5:S7. 2011
    ..Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies...
  23. ncbi request reprint Chromosomes, conflict, and epigenetics: chromosomal speciation revisited
    Judith D Brown
    Department of Allied Health Sciences, University of Connecticut, Storrs, CT 06269, USA
    Annu Rev Genomics Hum Genet 11:291-316. 2010
    ..In this review, we will examine both classical and current models of chromosomal speciation and describe the "evolving" theory of genetic conflict, epigenetics, and chromosomal speciation...