BMC Genomics Research article GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation Murat A Abdurashitov*, Valery A Chernukhin, Danila A Gonchar and Sergey Kh Degtyarev BioMed Central Open Access Address: SibEnzyme, 2/12 Ak. Timakov Str, 630117 Novosibirsk, Russia Email: Murat A Abdurashitov* - abd@sibenzyme.ru; Valery A Chernukhin - chernukhin@sibenzyme.ru; Danila A Gonchar - gonchar@sibenzyme.ru; Sergey Kh Degtyarev - degt@sibenzyme.com * Corresponding author Published: 17 July 2009 BMC Genomics 2009, 10:322 doi:10.1186/1471-2164-10-322 This article is available from: http://www.biomedcentral.com/1471-2164/10/322 Received: 4 December 2008 Accepted: 17 July 2009 © 2009 Abdurashitov et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dimer of γ-satellite DNA. Only small portion of mouse γ- satellite DNA sequences are presented in databases. Methyl-directed endonuclease GlaI cleaves mouse DNA and may be useful for a detailed study of primary structure and CG dinucleotides methylation in γ-satellite DNA. Results: We have constructed a physical map and produced experimental patterns of mouse γ- satellite DNA hydrolysis with unique site-specific methyl-directed endonuclease GlaI and several restriction endonucleases. Fifty two DNA fragments of γ-satellite DNA have been cloned and sequenced. We have not observed any mutations of CG dinucleotide in position 208 of monomeric γ-satellite DNA and confirmed 50% methylation of this CG dinucleoitide. A comparison of consensus sequences of arrayed γ-satellite DNA and small blocks of satellite DNA (140 monomers and less) has shown a higher level of mutations and an absence of conserved CG dinucleotide in last ones. A replacement of CG dinucleotide by CA-dinucleotide in positions 178 and 17 in chromosomes 9 and 3, respectively, has been observed in blocks of monomers. Conclusion: Arrayed γ-satellite DNA from mouse has at least one conservative CG-dinucleotide. Consensus sequences of this DNA and γ-satellite DNA in small blocks of monomers are differing. The last one displays a higher level of CG dinucleotides mutations and an absence of conservative CG-dinucleotide. Presence of conservative and half-methylated CG-dinucleotide supports an idea of importance of this CG dinucleotide methylation/demethylation in arrayed γ-satellite DNA functioning. Background Site-specific methyl-directed DNA endonuclease GlaI is the most interesting enzyme among new bacterial endo- nucleases, which cleave recognition sites with 5-methylcy- tosines and don't cut unmodified DNA [1-4]. GlaI substrates have been studied in details and include meth- Page 1 of 10 (page number not for citation purposes)