DNA Methylation

Marinus, Martin; Løbner-Olesen, Anders

doi:10.1128/ecosalplus.esp-0003-2013

Cited by 94 publications

(84 citation statements)

References 273 publications

(352 reference statements)

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“…Prokaryotes covalently modify their chromosomal DNA in several ways, the most common being methylation through base-specific methyltransferases (1). Methylation reactions occur at the N-6 position of adenine (methylated adenine [meA]) and the C-5 and N-4 positions of cytosine (m5C and m4C, respectively) using S -adenosylmethionine (SAM) as the methyl donor.…”

Section: Introductionmentioning

confidence: 99%

“…While the roles methylation plays in cells are broad (reviewed in references 1, 8, 9, 10, and 11), methylation by DNA adenine methyltransferase (Dam) (12) in Escherichia coli is necessary for proper cell cycle timing through methylation of oriC (13, 14), mismatch repair accuracy through discrimination between parental and newly synthesized DNA strands (15–17), regulation of transcription of a number of genes, including virulence factors (10), and regulation of transposition (18). Due to its role in regulation of transcription (4, 12), methylation is considered an epigenetic regulator (2, 9, 12).…”

Section: Introductionmentioning

confidence: 99%

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Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase

et al. 2016

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While it has been shown that methylation remains relatively constant into early stationary phase of E. coli, this study goes further through death phase and long-term stationary phase, a unique time in the bacterial life cycle due to nutrient limitation and strong selection for mutants with increased fitness. The absence of methylation at GATC sites can influence the mutation frequency within a population due to aberrant mismatch repair. Therefore, it is important to investigate the methylation status of GATC sites in an environment where cells may not prioritize methylation of the chromosome. This study demonstrates that chromosome methylation remains a priority even under conditions of nutrient limitation, indicating that continuous methylation at GATC sites could be under positive selection.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase

et al. 2016

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“…Except these REases and MTases, other proteins are able to interact with GATC, for example, MutH or SeqA. 34 However, these proteins are associated with Dam MTase and were found in all of the selected genomes with the dam gene and were not found in the genomes without the dam gene. 4,33 Thus, we did not analyze the in°uence of these proteins on GATC site representation separately.…”

Section: Introductionmentioning

confidence: 99%

“…12 Besides the fact that GATC is a recognition site of R-M systems, it is also related to di®erent processes in prokaryotic cells, which can also a®ect its representation in genomes. GATC site methylation by solitary Dam MTase is important for regulation of cell cycle as well as for regulation of some genes in E. coli and some other gamma proteobacteria, 1,34 in particular factors of virulence. 31 GATC sequence methylation is also associated with reparation of erroneously inserted nucleotides by the MutHLS mismatch repair complex.…”

Section: Introductionmentioning

confidence: 99%

“…34 Classical Type II R-M systems include MTases, which methylate the recognition sequence, and restriction endonucleases (REases), which hydrolyze unmethylated recognition site. Among MTases that recognize GATC sequence there are both adenine MTases, which methylate N6 of the adenine, 27,47 and cytosine MTases, which methylate either N4 or C5 positions of the cytosine 6,44 (N6mA, N4mC or 5mC MTases, correspondingly).…”

Section: Introductionmentioning

confidence: 99%

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Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes

Ershova

Rusinov

Vasiliev

et al. 2016

J. Bioinform. Comput. Biol.

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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. 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.

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An undergraduate laboratory on RNA sequencing analysis of bacterial gene expression

Militello

Reinhardt

2019

Biochem Molecular Bio Educ

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Next generation sequencing has revolutionized molecular biology and has provided a mechanism for rapid DNA and RNA sequence analysis. Yet, there are few resources to introduce next generation sequencing into the undergraduate biochemistry and molecular biology curriculum. Herein, we describe the design, execution, and assessment of a four-week laboratory for junior and senior undergraduate students that focuses on bacterial gene expression changes detected by RNA sequencing (RNA-seq). In the laboratory, students analyze a bacterial RNA-seq dataset in detail and answer questions relating to the impact of DNA methylation on bacterial gene expression. In addition, students confirm key results from the RNA-seq dataset using qRT-PCR and compare their results to similar experiments in the literature. A major strength of the laboratory is the ability of students to analyze raw RNA-seq data. In addition, another strength of the laboratory is the utilization of both dry approaches (informatics and statistics) and wet approaches (RNA isolation, cDNA synthesis, and qRT-PCR) to answer bacterial gene expression questions. Assessment of the laboratory indicates that significant learning gains were achieved with respect to next generation sequencing and RNA-seq. We expect that the laboratory will be a valuable resource as is, or via modification with other datasets and projects.

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DNA Methylation

Cited by 94 publications

References 273 publications

Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase

Genomewide Dam Methylation in Escherichia coli during Long-Term Stationary Phase

Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes

An undergraduate laboratory on RNA sequencing analysis of bacterial gene expression

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