Список литературы
- Usdin K. The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res. 2008;18:1011–1019. doi: 10.1101/gr.070409.107
- Haubold B., Wiehe T. How repetitive are genomes? BMC Bioinform. 2006;7. Article No. 541. doi: 10.1186/1471-2105-7-541
- Yi H., Song H., Hwang J., Kim K., Nierman W.C., Kim H.S. The tandem repeats enabling reversible switching between the two phases of β-lactamase substrate spectrum. PLoS Genet. 2014;10. Article No. e1004640. doi: 10.1371/journal.pgen.1004640
- Bulik-Sullivan B., Finucane H.K., Anttila V., Gusev A., Day F.R., Loh P.R. ReproGen Consortium, Psychiatric Genomics Consortium, Genetic Consortium for Anorexia Nervosa of the Wellcome Trust Case Control Consortium 3, Duncan L., et al. An atlas of genetic correlations across human diseases and traits. Nat. Genet. 2015;47:1236–1241. doi: 10.1038/ng.3406
- O’Dushlaine C.T., Edwards R.J., Park S.D., Shields D.C. Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol. 2005;6. Article No. R69. doi: 10.1186/gb-2005-6-8-r69
- Hannan A.J. Tandem repeat polymorphisms: Mediators of genetic plasticity modulators of biological diversity and dynamic sources of disease susceptibility. Adv. Exp. Med. Biol. 2012;769:1–9. doi: 10.1007/978-1-4614-5434-2_1
- Liao X., Zhu W., Zhou J., Li H., Xu X., Zhang B., Gao X. Repetitive DNA sequence detection and its role in the human genome. Commun. Biol. 2023;6. Article No. 954. doi: 10.1038/s42003-023-05322-y
- Liao X., Li M., Zou Y., Wu F.-X., Yi-Pan, Wang J. Current challenges and solutions of de novo assembly. Quant. Biol. 2019;7:90–109. doi: 10.1007/s40484-019-0166-9
- Jain C., Rhie A., Hansen N.F., Koren S., Phillippy A.M. Long-read mapping to repetitive reference sequences using Winnowmap2. Nat. Methods. 2022;19(6):705–710. doi: 10.1038/s41592-022-01457-8
- Jakubosky D., D'Antonio M., Bonder M.J., Smail C., Donovan M.K.R., Young Greenwald W.W., Matsui H., i2QTL Consortium, D'Antonio-Chronowska A., Stegle O., et al. Properties of structural variants and short tandem repeats associated with gene expression and complex traits. Nat. Commun. 2020;11(1). Article No. 2927. doi: 10.1038/s41467-020-16482-4
- Gymrek M., Willems T., Reich D., Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat. Genet. 2017;49(10):1495–1501. doi: 10.1038/ng.3952
- Castillo-Lizardo M., Henneke G., Viguera E. Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi. Front. Microbiol. 2014;5. Article No. 403. doi: 10.3389/fmicb.2014.00403
- Aguilar M., Prieto P. Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding. Front. Plant Sci. 2021;12. Article No. 672489. doi: 10.3389/fpls.2021.672489
- Lim C.J., Cech T.R. Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization. Nat. Rev. Mol. Cell Biol. 2021;22:283–298. doi: 10.1038/s41580-021-00328-y
- Lamb J.C., Birchler J.A. The role of DNA sequence in centromere formation. Genome Biol. 2003;4. Article No. 214. doi: 10.1186/gb-2003-4-5-214
- Miga K.H., Alexandrov I.A. Variation and evolution of human centromeres: a field guide and perspective. Ann. Rev. Genet. 2021;55:583–602. doi: 10.1146/annurev-genet-071719-020519
- Ishiura H., Doi K., Mitsui J., Yoshimura J., Matsukawa M.K., Fujiyama A., Toyoshima Y., Kakita A., Takahashi H., Suzuki Y., et al. Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy. Nat. Genet. 2018;50:581–590. doi: 10.1038/s41588-018-0067-2
- Albertin C.B., Simakov O., Mitros T., Wang Z.Y., Pungor J.R., Edsinger-Gonzales E., Brenner S., Ragsdale C.W., Rokhsar D.S. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 2015;524:220–224. doi: 10.1038/nature14668
- Sultanov D., Hochwagen A. Varying strength of selection contributes to the intragenomic diversity of rRNA genes. Nat. Commun. 2022;13. Article No. 7245. doi: 10.1038/s41467-022-34989-w
- Höweler C.J., Busch H.F.M., Geraedts J.P.M., Niermeijer M.F., Staal A. Anticipation in myotonic dystrophy: fact or fiction? Brain. 1989;112(3):779–797. doi: 10.1093/brain/112.3.779
- Taylor J.P., Brown Jr. R.H., Cleveland D.W. Decoding ALS: from genes to mechanism. Nature. 2016;539:197–206. doi: 10.1038/nature20413
- Fotsing S.F., Margoliash J., Wang C., Saini S., Yanicky R., Shleizer-Burko S., Goren A., Gymrek M. The impact of short tandem repeat variation on gene expression. Nat. Genet. 2019;51(11):1652–1659. doi: 10.1038/s41588-019-0521-9
- Gemayel R., Vinces M.D., Legendre M., Verstrepen K.J. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu. Rev. Genet. 2010;44:445–477. doi: 10.1146/annurev-genet-072610-155046
- Mukamel R.E., Handsaker R.E., Sherman M.A., Barton A.R., Zheng Y., McCarroll S.A., Loh P.R. Protein-coding repeat polymorphisms strongly shape diverse human phenotypes. Science. 2021;373(6562):1499–1505. doi: 10.1126/science.abg8289
- Fueyo R., Judd J., Feschotte C., Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat. Rev. Mol. Cell Biol. 2022;23(7):481–497. doi: 10.1038/s41580-022-00457-y
- Gemayel R., Cho J., Boeynaems S., Verstrepen K.J. Beyond junk-variable tandem repeats as facilitators of rapid evolution of regulatory and coding sequences. Genes (Basel). 2012;3(3):461–480. doi: 10.3390/genes3030461
- Shi Y., Niu Y., Zhang P., Luo H., Liu S., Zhang S., Wang J., Li Y., Liu X., Song T., et al. Characterization of genome-wide STR variation in 6487 human genomes. Nat. Commun. 2023;14(1). Article No. 2092. doi: 10.1038/s41467-023-37690-8
- Schröder C., Horsthemke B., Depienne C. GC-rich repeat expansions: associated disorders and mechanisms. Med. Genet. 2022;33(4):325-335. doi: 10.1515/medgen-2021-2099
- Mandel J.L. Breaking the rule of three. Nature. 1997;386:767–768. doi: 10.1038/386767a0
- Lalioti M.D., Scott H.S., Buresi C., Rossier C., Bottani A., Morris M.A., Malafosse A., Antonarakis S.E.. Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy. Nature. 1997;386:847–851. doi: 10.1038/386847a0
- Liquori C.L., Ricker K., Moseley M.L., Jacobsen J.F, Kress W., Naylor S.L., Day J.W., Ranum L.P.W. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science. 2001;293:864–867. doi: 10.1126/science.106212
- Matsuura T., Fang P., Pearson C.E., Jayakar P., Ashizawa T., Roa B.B., D.L. Nelson. Interruptions in the expanded ATTCT repeat of spinocerebellar ataxia type 10: repeat purity as a disease modifier? Am. J. Hum. Genet. 2006;78:125–129. doi: 10.1086/498654
- Richard G.F., Kerrest A., Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol. Mol. Biol. Rev. 2008;72:686–727. doi: 10.1128/MMBR.00011-08
- Baran N., Lapidot A., Manor H. Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts. Proc. Natl. Acad. Sci. USA. 1991;88:507–511. doi: 10.1073/pnas.88.2.507
- Arimondo P.B., Barcelo F., Sun J.S., Maurizot J.C., Garestier T., Helene C. Triple helix formation by (G,A)-containing oligonucleotides: asymmetric sequence effect. Biochemistry. 1998;37:16627–16635. doi: 10.1021/bi9805588
- Rippe K., Fritsch V., Westhof E., Jovin T.M. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 1992;11(10):3777–3786. doi: 10.1002/j.1460-2075.1992.tb05463.x
- Huertas D., Azorín F. Structural Polymorphism of Homopurine DNA Sequences. d(GGA)n and d(GGGA)n Repeats Form Intramolecular Hairpins Stabilized by Different Base-Pairing Interactions. Biochemistry. 1996;35:13125–13135. doi: 10.1021/bi961020+
- Shiber M.C., Braswell E.H., Klump H., Fresco J.R. Duplex-tetraplex equilibrium between a hairpin and two interacting hairpins of d(A-G)10 at neutral pH. Nucleic Acids Res. 1996;24(24):5004–5012. doi: 10.1093/nar/24.24.5004
- Videvall E. Plasmodium parasites of birds have the most AT-rich genes of eukaryotes. Microb. Genom. 2018;4(2). Article No. e000150. doi: 10.1099/mgen.0.000150
- Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 1985;228(4702):953–958. doi: 10.1126/science.4001930
- Hurst L.D., Merchant A.R. High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc. Biol. Sci. 2001;268:493–497. doi: 10.1098/rspb.2000.1397
- Tetuev R.K., Nazipova N.N., Pankratov A.N., Dedus F.F. Search for Megasatellite Tandem Repeats in Eukaryotic Genomes by Estimation of GC-content Curve Oscillations. Маthematical Biology and Bioinformatics. 2010;5(1):30–42. doi: 10.17537/2010.5.30
- Pankratov A.N., Gorchakov M.A., D.A.Dedus F.F., Dolotova N.S., Kulikova L.I., Makhortykh S.A., Nazipova N.N., Novikova, Olshevets M.M., Pyatkov M.I., et al. Spectral Analysis for Identification and Visualization of Repeats in Genetic Sequences. Pattern Recognition and Image Analysis. 2009;19(4):687–692. doi: 10.1134/S105466180904018X
- Tetuev R.K., Nazipova N.N. Consensus of repeated region of mouse chromosome 6 containing 60 tandem copies of a complex pattern. Repbase Reports. 2010;10(5):776–776. doi: 10.1525/bio.2010.60.10.fm
- Tetuev R.K., Dedus F.F., Nazipova N.N. Consensus of repeated region of rat chromosome 4 similar to mouse chromosome 6 repeated region, enclosed in the intergenic region between genes Hrh1 and Atg7. Repbase Reports. 2010;10(8):1185–1185.
- Liu J., Li Q., Hu Y., Yu Y., Zheng K., Li D., Qin L., Yu X. The complete telomere-to-telomere sequence of a mouse genome. Science. 2024;386(6726):1141–1146. doi: 10.1126/science.adq8191
- Tetuev R.K., Nazipova N.N. Fast 2Bit-Encoding for DNA Sequences in the TANDIS searching system. In: Proceedings of the International Conference “Mathematical Biology and Bioinformatics”. Ed. V.D. Lakhno. Vol. 10. Pushchino: IMPB RAS, 2024. Paper No. e43. doi: 10.17537/icmbb24.59
- Dedus F.F., Kulikova L.I., Makhortykh S.A., Nazipova N.N., Pankratov A.N., Tetuev R.K. Analytical recognition methods for repeated structures in genomes. Doklady Mathematics. 2006;74(3):926–929. doi: 10.1134/S1064562406060354
- Tetuev R.K. Algebra of spectral transforms in data processing problems: PhD Thesis. M.: Computing Center of the Russian Academy of Sciences, 2007 (in Russ.).
- Zhang Z., Schwartz S., Wagner L., Miller W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 2000;7(1–2):203–214. doi: 10.1089/10665270050081478
- Madeira F., Madhusoodanan N., Lee J., Eusebi A., Niewielska A., Tivey A.R.N., Lopez R., Butcher S. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research. 2024;52(W1):W521–W525. doi: 10.1093/nar/gkae241
- Jeffreys A.J., Murray J., Neumann R. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot. Mol. Cell. 1998;2(2):267–273. doi: 10.1016/S1097-2765(00)80138-0
- Strand M., Prolla T.A., Liskay R.M., Petes T.D. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature. 1993;365(6443):274–276. doi: 10.1038/365274a0
- Xu X., Peng M., Fang Z. The direction of microsatellite mutations is dependent upon allele length. Nat. Genet. 2000;24(4):396–399. doi: 10.1038/74238
- Calabrese P.P., Durrett R.T., Aquadro C.F. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics. 2001;159(2):839–852. doi: 10.1093/genetics/159.2.839
- Santibáñez-Koref M.F., Gangeswaran R., Hancock J.M. A relationship between lengths of microsatellites and nearby substitution rates in mammalian genomes. Mol. Biol. Evol. 2001;18(11):2119–2123. doi: 10.1093/oxfordjournals.molbev.a003753
- Duret L., Galtier N. Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes. Annual Review of Genomics and Human Genetics. 2009;10:285–311. doi: 10.1146/annurev-genom-082908-150001
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