Our research focus is to understand the structure and function of unusual DNA sequences in living cells, and how these sequences cause genome instability and lead to human diseases. Human chromosomal fragile sites have been correlated with the chromosomal deletions and gene rearrangements found in many cancers. Our studies are aimed at understanding the genesis of breakpoints that occur at or near fragile sites during oncogenesis.
Ongoing projects include:
(I) Genome-wide DNA Secondary Structure Analysis to Investigate DNA Fragility (supported by RO1 GM101192-01A1, July 1, 2013- June 30, 2017)
Chromosomal fragile sites, which are regions of the genome that exhibit chromosomal breakage under conditions of mild replication stress, are predicted to form stable DNA secondary structures. We have developed a protocol can narrow down sites of true fragility within the current cytogenetically-defined fragile sites, and uncover potential new fragile sites previously unidentified or too small to be observed cytogenetically. The ultimate goal is to create a list of legitimate sites that are prone to DNA breakage caused by the secondary structure-forming mechanism(s), to evaluate genomic stress caused by endogenous and exogenous insults.
Thys RG, Lehman CE, Pierce LC, Wang YH. Environmental and chemotherapeutic agents induce breakage at genes involved in leukemia-causing gene rearrangements in human hematopoietic stem/progenitor cells. Mutat Res. 2015 Sep;779:86-95. PubMed PMID: 26163765.
Thys RG, Lehman CE, Pierce LC, Wang YH. DNA secondary structure at chromosomal fragile sites in human disease. Curr Genomics. 2015 Feb;16(1):60-70. PubMed PMID: 25937814; PubMed Central PMCID: PMC4412965.
Dillon LW, Pierce LC, Ng MC, Wang YH. Role of DNA secondary structures in fragile site breakage along human chromosome 10. Hum Mol Genet. 2013 Apr 1;22(7):1443-56. PubMed PMID: 23297364; PubMed Central PMCID: PMC3596854.
Burrow AA, Marullo A, Holder LR, Wang YH. Secondary structure formation and DNA instability at fragile site FRA16B. Nucleic Acids Res. 2010 May;38(9):2865-77. PubMed PMID: 20071743; PubMed Central PMCID: PMC2875025.
Burrow AA, Williams LE, Pierce LC, Wang YH. Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites. BMC Genomics. 2009 Jan 30;10:59. PubMed PMID: 19183484; PubMed Central PMCID: PMC2642838.
(II) Roles of fragile sites in cancer-causing gene rearrangements (supported by RO1CA113863,Oct 1, 2015 – Sept 2019)
Using thyroid cancer as a model, we investigate the involvement of DNA fragility in the generation of non-radiation-related chromosomal rearrangements in human cells. We demonstrated that fragile sites participate in the generation of RET/PTC rearrangement in thyroid cells, and this allows exploration of the mechanisms of fragility in these regions to extend our understanding of the molecular mechanisms of chromosomal rearrangements in cancer cells.
Dillon LW, Pierce LC, Lehman CE, Nikiforov YE, Wang YH. DNA topoisomerases participate in fragility of the oncogene RET. PLoS One. 2013;8(9):e75741. PubMed PMID: 24040417; PubMed Central PMCID: PMC3770543.
Gandhi M, Dillon LW, Pramanik S, Nikiforov YE, Wang YH. DNA breaks at fragile sites generate oncogenic RET/PTC rearrangements in human thyroid cells. Oncogene. 2010 Apr 15;29(15):2272-80. PubMed PMID: 20101222; PubMed Central PMCID: PMC2855398.
(III) Alternative DNA/RNA secondary structure in genetic diseases.
Over 30 human diseases, mostly neurological and muscular, are associated with expansion of repetitive DNA sequences. Repetitive DNA sequences have the ability to form a variety of secondary structures during normal cellular processes such as replication and transcription due to the unwinding of duplex DNA. Through collaborations, we investigate the mechanism for repeat expansion and disease pathogenesis.
Reddy K, Schmidt MH, Geist JM, Thakkar NP, Panigrahi GB, Wang YH, Pearson CE. Processing of double-R-loops in (CAG)·(CTG) and C9orf72 (GGGGCC)·(GGCCCC) repeats causes instability. Nucleic Acids Res. 2014;42(16):10473-87. PubMed PMID: 25147206; PubMed Central PMCID: PMC4176329.
Axford MM, Wang YH, Nakamori M, Zannis-Hadjopoulos M, Thornton CA, Pearson CE. Detection of slipped-DNAs at the trinucleotide repeats of the myotonic dystrophy type I disease locus in patient tissues. PLoS Genet. 2013;9(12):e1003866. PubMed PMID: 24367268; PubMed Central PMCID: PMC3868534.
Reddy K, Tam M, Bowater RP, Barber M, Tomlinson M, Nichol Edamura K, Wang YH, Pearson CE. Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Res. 2011 Mar;39(5):1749-62. PubMed PMID: 21051337; PubMed Central PMCID: PMC3061079.