Rachel J. O’Neill
A5015873205- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Animal Genetics and Reproduction
- RNA and protein synthesis mechanisms
- Genomic variations and chromosomal abnormalities
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Bat Biology and Ecology Studies
- RNA Research and Splicing
- Genetic Syndromes and Imprinting
- Cancer-related molecular mechanisms research
- Reproductive Biology and Fertility
- Plant Virus Research Studies
- Genetic and phenotypic traits in livestock
- Physiological and biochemical adaptations
- Plant Molecular Biology Research
- Advanced biosensing and bioanalysis techniques
- Molecular Biology Techniques and Applications
- Sperm and Testicular Function
- Primate Behavior and Ecology
University of Connecticut
2016-2025
UConn Health
2021-2025
CURE International UK
2024
Institute for Systems Biology
2014-2023
National University of Ireland, Maynooth
2022-2023
Queen's University Belfast
2012-2021
University of North Carolina at Chapel Hill
2008-2021
Parsons School of Design
2015
NewSchool of Architecture and Design
2015
New School
2015
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric centromeric repeats, constitute 6.2% the (189.9 megabases). Detailed maps these regions revealed multimegabase structural...
Sexual isolation is a critical form of reproductive in the early stages animal speciation, yet little known about genetic basis divergent mate preferences and preference cues young species. Heliconius butterflies, well for their diversity wing color patterns, assortatively as result divergence male patterns. Here we show that specific cue used by cydno pachinus males to recognize conspecific females patches on wings. In addition, segregates with forewing hybrids, indicating association...
Mobile elements and repetitive genomic regions are sources of lineage-specific innovation uniquely fingerprint individual genomes. Comprehensive analyses such repeat elements, including those found in more complex the genome, require a complete, linear genome assembly. We present de novo discovery annotation T2T-CHM13 human reference genome. identified previously unknown satellite arrays, expanded catalog variants families for repeats mobile characterized classes composite repeats, located...
November 2020 marked 2 y since the launch of Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across aspects EBP roadmap, as outlined 2018 article describing project’s goals, strategies, and challenges (1). The phase ended clock started on reaching EBP’s major milestones. This Special Feature explores many facets EBP, including review progress, description scientific exemplar projects,...
The koala, the only extant species of marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced koala genome, producing a complete contiguous reference including centromeres. reveal that koala's ability detoxify eucalypt foliage may be expansions within cytochrome P450 gene family, its smell, taste moderate ingestion plant secondary metabolites in vomeronasal receptors. characterized novel lactation proteins protect young pouch...
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions the including repetitive and homologous regions. Here, we present high-resolution epigenetic study previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, diverse collection repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, short-read datasets (166,058 chromatin immunoprecipitation...
During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete has not been possible until Next Generation Sequencing Technology.Here we report comprehensive transcriptome dynamics single matured bovine oocytes embryos developed vivo. Surprisingly, more than half estimated 22,000 genes, 11,488 to 12,729 involved 100 pathways, is expressed early embryos. Despite similarity total numbers genes across...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology...
Abstract Background We present the genome sequence of tammar wallaby, Macropus eugenii , which is a member kangaroo family and first representative iconic hopping mammals that symbolize Australia to be sequenced. The has many unusual biological characteristics, including longest period embryonic diapause any mammal, extremely synchronized seasonal breeding prolonged sophisticated lactation within well-defined pouch. Like other marsupials, it gives birth highly altricial young, small number...
Heterochromatin formed by the SUV39 histone methyltransferases represses transcription from repetitive DNA sequences and ensures genomic stability. How enzymes localize to their target loci remains unclear. Here, we demonstrate that chromatin-associated RNA contributes stable association of SUV39H1 with constitutive heterochromatin in human cells. We find associated mitotic chromosomes is concentrated at pericentric heterochromatin, encoded, part, α-satellite sequences, which are retained...
During routine screens of the NCBI databases using human repetitive elements we discovered an unlikely level nucleotide identity across a broad range phyla. To ascertain whether containing DNA sequences, genome assemblies and trace archive reads were contaminated with performed in depth search for sequences origin non-human species. Using primate specific SINE, AluY, screened 2,749 non-primate public from NCBI, Ensembl, JGI, UCSC have found 492 to be sequence. These represent species ranging...
The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into modern era. Despite last sharing a common ancestor with eutherian canids ~160 million years ago, their phenotypic resemblance is considered most striking example of convergent evolution in mammals. known died captivity 1936 and many aspects evolutionary history this unique apex predator remain unknown. Here we have sequenced genome preserved pouch young specimen clarify...
The relationship between evolutionary genome remodeling and the three-dimensional structure of remain largely unexplored. Here, we use heavily rearranged gibbon to examine how chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), their epigenetic landscape. We high-resolution maps gibbon-human breaks synteny (BOS), apply Hi-C in gibbon, measure an array features, perform cross-species comparisons. find that occur at TAD boundaries,...
Abstract Centromere location is specified by CENP-A, a centromere-specific histone that epigenetically propagates centromere identity. How CENP-A maintained at one in rapidly evolving centromeric DNA unknown. Using single cell-derived clones of human cell lines, we demonstrate heterogeneity position within populations neocentromeres and native centromere. accompanied heterogenous methylation H3K9me3 patterns, with shifting according to position. We further reveal temporary precise...