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Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2016,4]]},"abstract":"<jats:p>Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes.<\/jats:p><jats:p>In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.<\/jats:p>","DOI":"10.1142\/s0219720016410031","type":"journal-article","created":{"date-parts":[[2016,2,24]],"date-time":"2016-02-24T02:35:24Z","timestamp":1456281324000},"page":"1641003","source":"Crossref","is-referenced-by-count":3,"title":["Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes"],"prefix":"10.1142","volume":"14","author":[{"given":"Anna","family":"Ershova","sequence":"first","affiliation":[{"name":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia"},{"name":"Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia"},{"name":"Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, 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