Copy number variation (CNV) is a significant source of genomic diversity and human disease9,10. Subtelomeric CNVs are large deletions, duplications, and translocations that occur at chromosome ends and are responsible for 3-6% of idiopathic mental retardation cases6,11-13. Individuals with subtelomeric rearrangements have intellectual disabilities, autism, dysmorphic features, and/or other birth defects. Children are typically diagnosed with a subtelomeric rearrangement using cytogenetic tests such as subtelomeric fluorescence in situ hybridization (FISH) or array comparative genomic hybridization (CGH). Subtelomeric rearrangements have been estimated to account for up to 30% of pathogenic CNVs detected in affected children9,14, and the overall prevalence of subtelomeric rearrangements is estimated at 1/10,00015. Despite the impact on human health, very little is known about the mechanisms of chromosome breakage and repair that give rise to subtelomeric CNV. Research on the fundamental biology of CNV formation is critical to understanding the causes of and risk factors associated with disease-causing structural rearrangements. We hypothesize that particular DNA sequences are susceptible to breakage. To this end, we propose to isolate human DNA sequences that underlie subtelomeric breakage sites and functionally dissect the motifs that cause double-strand breaks (DSBs).
The aims of this proposal are to 1) fine-map subtelomeric breakpoints, 2) identify subtelomeric sequence motifs that contribute to genomic instability, and 3) functionally annotate breakage motifs in a yeast gross chromosomal rearrangement (GCR) assay that quantifies chromosome breakage in the subtelomeric sequence. Integrated genomic, bioinformatics, and in vivo breakage experiments will determine whether or not DNA sequence plays a role in subtelomeric breakage. Our studies will also capture the genomic structure of subtelomeric rearrangements, which will allow us to determine the mechanisms of repair acting on subtelomeric DSBs. This proposal promises to reveal new sequence motifs that promote genomic instability and novel mechanisms of DNA repair. These data will be critical to understanding the forces that shape subtelomeric rearrangements and other CNV throughout the human genome.
Subtelomeric rearrangements, which occur at the ends of chromosomes, are a significant cause of intellectual disability and birth defects. We propose to sequence subtelomeric breakpoints and identify sequence motifs that promote genomic instability. We will determine the fragility of subtelomeric sequence motifs by introducing them into a yeast assay that measures chromosome breakage.
|Guilherme, Roberta Santos; Hermetz, Karen E; Varela, Patrícia Teixeira et al. (2015) Terminal 18q deletions are stabilized by neotelomeres. Mol Cytogenet 8:32|
|Weckselblatt, Brooke; Hermetz, Karen E; Rudd, M Katharine (2015) Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Res 25:937-47|
|Weckselblatt, Brooke; Rudd, M Katharine (2015) Human Structural Variation: Mechanisms of Chromosome Rearrangements. Trends Genet 31:587-599|
|Newman, Scott; Hermetz, Karen E; Weckselblatt, Brooke et al. (2015) Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. Am J Hum Genet 96:208-20|
|Riley, Kacie N; Catalano, Lisa M; Bernat, John A et al. (2015) Recurrent deletions and duplications of chromosome 2q11.2 and 2q13 are associated with variable outcomes. Am J Med Genet A 167A:2664-73|
|Bose, Promita; Hermetz, Karen E; Conneely, Karen N et al. (2014) Tandem repeats and G-rich sequences are enriched at human CNV breakpoints. PLoS One 9:e101607|
|Hermetz, Karen E; Newman, Scott; Conneely, Karen N et al. (2014) Large inverted duplications in the human genome form via a fold-back mechanism. PLoS Genet 10:e1004139|
|Goldlust, Ian S; Hermetz, Karen E; Catalano, Lisa M et al. (2013) Mouse model implicates GNB3 duplication in a childhood obesity syndrome. Proc Natl Acad Sci U S A 110:14990-4|
|Mason-Suares, Heather; Kim, Wayne; Grimmett, Leslie et al. (2013) Density matters: comparison of array platforms for detection of copy-number variation and copy-neutral abnormalities. Genet Med 15:706-12|
|Wang, Tao; Wu, Hao; Li, Yujing et al. (2013) Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nat Cell Biol 15:700-11|
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