Isolation and Characterization of Biochemical Properties of DNA Methyltransferase FauIA Modifying the Second Cytosine in the Nonpalindromic Sequence 5′-CCCGC-3′

Chernukhin, V. A.; Kashirina, Yu. G.; Sukhanova, K. S.; Abdurashitov, M. A.; Gonchar, D. A.; Degtyarev, S. Kh.

doi:10.1007/s10541-005-0169-1

Cited by 4 publications

(2 citation statements)

References 17 publications

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“…For example, it is reported that both methylases (LlaDII and Bsp6I R/M) have two recognition sites (5'-GCGGC-3' and 5'-GCCGC-3') [18]. DNA methyltransferase (methylase) FauIA (of the restriction-modification system FauI from Flavobacterium aquatile)'s recognization site is 5'-CCCGC-3' [19]. Our study offers a perspective to find a connection between the DNA sequence fragments and the methylation mechanism.…”

Section: Resultsmentioning

confidence: 99%

Predicting DNA methylation status using word composition

Lu¹,

Lin²,

Zhou³

et al. 2010

JBiSE

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Background: DNA methylation will influence the gene expression pattern and cause the changes of the genetic functions. Computational analysis of the methylation status for nucleotides can help to explore the underlying reasons for developing methylations. Results: We present a DNA sequence based method to analyze the methylation status of CpG dinucleotides using 5bp (5-mer) DNA fragments – named as the word composition encoding method. The prediction accuracy is 75.16% when all 5bp word compositions are used (totally 45 = 1024). Furthermore, 5-bp DNA fragments/words having the most impact on the methylation status are identified by mRMR (Maximum-Relevant-Minimum-Redundancy) feature selection method. As a result, 58 words are selected, and they are used to build a compact predictor, which achieves 77.45% prediction accuracy. When the word composition encoding method and the feature selection strategy are coupled together, the meaning of these words can be analyzed through their contribution towards the prediction. The biological evidence in the literature supports that the surrounding DNA sequence of the CpG dinucleotides will affect the methylation of the CpG dinucleotides. Conclusions: The main contribution of this paper is to find out and analyze the key DNA words taken from the neighbor-hood of the CpG dinucleotides that are inducing the DNA methylation

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Section: Resultsmentioning

confidence: 99%

Predicting DNA methylation status using word composition

Lu¹,

Lin²,

Zhou³

et al. 2010

JBiSE

View full text Add to dashboard Cite

show abstract

“…It has also been shown that 5 bp DNA lengths are important for DNA methylation where they are probably associated with the binding of DNA methyltransferase [29]. 5 bp long sequences are important for the binding of many enzymes including the methyltransferase; both methylases ( Lla DII and Bsp 6I R/M) have two recognition sites (5′-GCGGC-3′ and 5′-GCCGC-3′) [3-0] and 5′-CCCGC-3′ is the recognition site of the DNA methyltransferase (methylase) FauIA (of the restriction-modification system FauI from Flavobacterium aquatile ) [30]. …”

Section: Methodsmentioning

confidence: 99%

Comparative (Computational) Analysis of the DNA Methylation Status of Trinucleotide Repeat Expansion Diseases

Ghorbani

Taylor

Pook

et al. 2013

Journal of Nucleic Acids

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Previous studies have examined DNA methylation in different trinucleotide repeat diseases. We have combined this data and used a pattern searching algorithm to identify motifs in the DNA surrounding aberrantly methylated CpGs found in the DNA of patients with one of the three trinucleotide repeat (TNR) expansion diseases: fragile X syndrome (FRAXA), myotonic dystrophy type I (DM1), or Friedreich's ataxia (FRDA). We examined sequences surrounding both the variably methylated (VM) CpGs, which are hypermethylated in patients compared with unaffected controls, and the nonvariably methylated CpGs which remain either always methylated (AM) or never methylated (NM) in both patients and controls. Using the J48 algorithm of WEKA analysis, we identified that two patterns are all that is necessary to classify our three regions CCGG∗ which is found in VM and not in AM regions and AATT∗ which distinguished between NM and VM + AM using proportional frequency. Furthermore, comparing our software with MEME software, we have demonstrated that our software identifies more patterns than MEME in these short DNA sequences. Thus, we present evidence that the DNA sequence surrounding CpG can influence its susceptibility to be de novo methylated in a disease state associated with a trinucleotide repeat.

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Substrate specificity and biochemical properties of M3.BstF5I DNA methyltransferase from the BstF5I restriction-modification system

Chernukhin¹,

Kuznetsov

Gonchar³

et al. 2010

Biochemistry Moscow

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Optimal conditions for DNA methylation by the M3.BstF5I enzyme from Bacillus stearothermophilus and kinetic parameters of lambda phage DNA modification and that of a number of oligonucleotide substrates are established. Comparison of M1.BstF5I and M3.BstF5I kinetic parameters revealed that with similar temperature optima and affinity for DNA, M3.BstF5I has nearly fourfold lower turnover number (0.24 min(-1)) and modifies the hemimethylated recognition site with lower efficiency under optimal conditions than the unmethylated one. In contrast to another three methylases of the BstF5I restriction-modification system, the M3.BstF5I enzyme is able to optionally modify the noncanonical 5'-GGATC-3' DNA sequence with a rate more than one order of magnitude lower than the methylation rate of the canonical 5'-GGATG-3' recognition site.

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Isolation and Characterization of Biochemical Properties of DNA Methyltransferase FauIA Modifying the Second Cytosine in the Nonpalindromic Sequence 5′-CCCGC-3′

Cited by 4 publications

References 17 publications

Predicting DNA methylation status using word composition

Predicting DNA methylation status using word composition

Comparative (Computational) Analysis of the DNA Methylation Status of Trinucleotide Repeat Expansion Diseases

Substrate specificity and biochemical properties of M3.BstF5I DNA methyltransferase from the BstF5I restriction-modification system

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