Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). The most recent and compete human genome sequencing assembly reveals more repetitive elements in the human genome than researchers have previously estimated, which could potentially support non-B DNA formation.
Article CAS PubMed PubMed Central Google Scholar
Plohl, M., Luchetti, A., Mestrovic, N. & Mantovani, B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409, 72–82 (2008).
Article CAS PubMed Google Scholar
Thakur, J., Packiaraj, J. & Henikoff, S. Sequence, chromatin and evolution of satellite DNA. Int. J. Mol. Sci. 22, 4309 (2021).
Article CAS PubMed PubMed Central Google Scholar
Herbert, A. ALU non-B-DNA conformations, flipons, binary codes and evolution. R. Soc. Open. Sci. 7, 200222 (2020).
Article CAS PubMed PubMed Central Google Scholar
Kasinathan, S. & Henikoff, S. Non-B-form DNA is enriched at centromeres. Mol. Biol. Evol. 35, 949–962 (2018).
Article CAS PubMed PubMed Central Google Scholar
Wang, G. & Vasquez, K. M. Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability. DNA Repair 19, 143–151 (2014).
Article PubMed PubMed Central Google Scholar
Choi, J. & Majima, T. Conformational changes of non-B DNA. Chem. Soc. Rev. 40, 5893–5909 (2011).
Article CAS PubMed Google Scholar
Guiblet, W. M. et al. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. Genome Res. 28, 1767–1778 (2018).
Article CAS PubMed PubMed Central Google Scholar
Marshall, P. R. et al. Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nat. Neurosci. 23, 718–729 (2020). The ADAR1 protein binds to Z-DNA in the mouse prefrontal cortex during fear extinction learning and supresses or reduces Z-DNA formation, which is suggested to be required for memory flexibility.
Article CAS PubMed PubMed Central Google Scholar
Mirkin, S. M. Expandable DNA repeats and human disease. Nature 447, 932–940 (2007).
Article CAS PubMed Google Scholar
Praseuth, D., Guieysse, A. L. & Helene, C. Triple helix formation and the antigene strategy for sequence-specific control of gene expression. Biochim. Biophys. Acta 1489, 181–206 (1999).
Article CAS PubMed Google Scholar
Huppert, J. L. & Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35, 406–413 (2007).
Article CAS PubMed Google Scholar
Marsico, G. et al. Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 47, 3862–3874 (2019).
Article CAS PubMed PubMed Central Google Scholar
Valton, A. L. & Prioleau, M. N. G-quadruplexes in DNA replication: a problem or a necessity? Trends Genet. 32, 697–706 (2016).
Article CAS PubMed Google Scholar
Wang, G. & Vasquez, K. M. Effects of replication and transcription on DNA structure-related genetic instability. Genes 8, 17 (2017).
Article CAS PubMed Central Google Scholar
Prioleau, M. N. G-quadruplexes and DNA replication origins. Adv. Exp. Med. Biol. 1042, 273–286 (2017).
Article CAS PubMed Google Scholar
St Germain, C., Zhao, H. & Barlow, J. H. Transcription-replication collisions — a series of unfortunate events. Biomolecules 11, 1249 (2021).
Liu, G., Chen, X., Bissler, J. J., Sinden, R. R. & Leffak, M. Replication-dependent instability at (CTG) x (CAG) repeat hairpins in human cells. Nat. Chem. Biol. 6, 652–659 (2010).
Article CAS PubMed PubMed Central Google Scholar
Gomes-Pereira, M., Fortune, M. T. & Monckton, D. G. Mouse tissue culture models of unstable triplet repeats: in vitro selection for larger alleles, mutational expansion bias and tissue specificity, but no association with cell division rates. Hum. Mol. Genet. 10, 845–854 (2001).
Article CAS PubMed Google Scholar
Fu, Y. H. et al. Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell 67, 1047–1058 (1991).
Article CAS PubMed Google Scholar
Kremer, E. J. et al. Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science 252, 1711–1714 (1991).
Article CAS PubMed Google Scholar
La Spada, A. R., Wilson, E. M., Lubahn, D. B., Harding, A. E. & Fischbeck, K. H. Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy. Nature 352, 77–79 (1991).
Catasus, L. et al. Frameshift mutations at coding mononucleotide repeat microsatellites in endometrial carcinoma with microsatellite instability. Cancer 88, 2290–2297 (2000).
Article CAS PubMed Google Scholar
Georgakopoulos-Soares, I. et al. Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts. Nat. Commun. 11, 1980 (2020). Using bioinformatic approaches, this study reports transcription-associated asymmetrical distribution of repetitive elements, insertions and deletions at repeats in human cancer genomes, with involvement of DNA repair pathways.
Article CAS PubMed PubMed Central Google Scholar
Rothenburg, S., Koch-Nolte, F., Rich, A. & Haag, F. A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity. Proc. Natl Acad. Sci. USA 98, 8985–8990 (2001).
Article CAS PubMed PubMed Central Google Scholar
Malik, I., Kelley, C. P., Wang, E. T. & Todd, P. K. Molecular mechanisms underlying nucleotide repeat expansion disorders. Nat. Rev. Mol. Cell Biol. 22, 589–607 (2021).
Article CAS PubMed PubMed Central Google Scholar
Paulson, H. L. & Fischbeck, K. H. Trinucleotide repeats in neurogenetic disorders. Annu. Rev. Neurosci. 19, 79–107 (1996).
Article CAS PubMed Google Scholar
McMurray, C. T. Mechanisms of trinucleotide repeat instability during human development. Nat. Rev. Genet. 11, 786–799 (2010).
Article CAS PubMed PubMed Central Google Scholar
Jones, L., Houlden, H. & Tabrizi, S. J. DNA repair in the trinucleotide repeat disorders. Lancet Neurol. 16, 88–96 (2017).
Article CAS PubMed Google Scholar
Cleary, J. D. & Pearson, C. E. Replication fork dynamics and dynamic mutations: the fork-shift model of repeat instability. Trends Genet. 21, 272–280 (2005).
Article CAS PubMed Google Scholar
McKinney, J. A. et al. Distinct DNA repair pathways cause genomic instability at alternative DNA structures. Nat. Commun. 11, 236 (2020). This study reports that the MMR protein complex MSH2–MSH3 binds to Z-DNA and recruits the NER nuclease ERCC1–XPF to the site, resulting in structure-specific cleavage and DSBs at Z-DNA regardless of DNA replication status.
Article CAS PubMed PubMed Central Google Scholar
Zhao, J. et al. Distinct mechanisms of nuclease-directed DNA-structure-induced genetic instability in cancer genomes. Cell Rep. 22, 1200–1210 (2018).
Article CAS PubMed PubMed Central Google Scholar
Iyer, R. R., Pluciennik, A., Napierala, M. & Wells, R. D. DNA triplet repeat expansion and mismatch repair. Annu. Rev. Biochem. 84, 199–226 (2015).
Article CAS PubMed PubMed Central Google Scholar
Sundararajan, R. & Freudenreich, C. H. Expanded CAG/CTG repeat DNA induces a checkpoint response that impacts cell proliferation in Saccharomyces cerevisiae. PLoS Genet. 7, e1001339 (2011). Long CAG/CTG repeats trigger an MRX-dependent DNA damage checkpoint response in budding yeast, which affects the cell cycle, leading to repeat-dependent S-phase delays and G2/M arrests, which results in morphological abnormalities.
Article CAS PubMed PubMed Central Google Scholar
Voineagu, I., Surka, C. F., Shishkin, A. A., Krasilnikova, M. M. & Mirkin, S. M. Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility. Nat. Struct. Mol. Biol. 16, 226–228 (2009).
留言 (0)