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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

Roberts RJ, Vincze T, Posfai J, Macelis D - Nucleic Acids Res. (2014)

Bottom Line: REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems.All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly.Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing.

View Article: PubMed Central - PubMed

Affiliation: New England Biolabs, Ipswich, MA 01938, USA roberts@neb.com.

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Dotted lines signify methylated motifs awaiting gene assignment. The sharp increase starting in 2012 is the result of the introduction of SMRT sequencing.
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Figure 1: Dotted lines signify methylated motifs awaiting gene assignment. The sharp increase starting in 2012 is the result of the introduction of SMRT sequencing.

Mentions: The fastest growing segment of biochemically characterized RM system components are the DNA methyltransferases, currently being found using real-time Single Molecule Real Time (SMRT) sequencing (5–7). In a large number of cases the recognition motifs for DNA methyltransferases arising from such sequencing can be matched with the genes that encode them. For instance, the recognition sequences of Type I systems have a very characteristic bipartite structure and when the genome contains only one such Type I set of genes, then it is clear that the methyltransferase gene and its associated specificity gene are both active and the recognition motif can be assigned. This in turn allows propagation of these specificities both to putative Type I systems and also in many cases allows the identification of active Type I systems in genomes where more than one Type I system is present. These matches are made via REBASE and documented. The same is true for Type III RM systems and again, is made possible because the recognition specificity for the system is encoded in the methyltransferase gene. The enormous growth in these systems is shown in Figure 1, which documents the rate of discovery of Type I and Type III RM system specificities since the very first one was discovered and characterized in 1968 (8).


REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.

Roberts RJ, Vincze T, Posfai J, Macelis D - Nucleic Acids Res. (2014)

Dotted lines signify methylated motifs awaiting gene assignment. The sharp increase starting in 2012 is the result of the introduction of SMRT sequencing.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383893&req=5

Figure 1: Dotted lines signify methylated motifs awaiting gene assignment. The sharp increase starting in 2012 is the result of the introduction of SMRT sequencing.
Mentions: The fastest growing segment of biochemically characterized RM system components are the DNA methyltransferases, currently being found using real-time Single Molecule Real Time (SMRT) sequencing (5–7). In a large number of cases the recognition motifs for DNA methyltransferases arising from such sequencing can be matched with the genes that encode them. For instance, the recognition sequences of Type I systems have a very characteristic bipartite structure and when the genome contains only one such Type I set of genes, then it is clear that the methyltransferase gene and its associated specificity gene are both active and the recognition motif can be assigned. This in turn allows propagation of these specificities both to putative Type I systems and also in many cases allows the identification of active Type I systems in genomes where more than one Type I system is present. These matches are made via REBASE and documented. The same is true for Type III RM systems and again, is made possible because the recognition specificity for the system is encoded in the methyltransferase gene. The enormous growth in these systems is shown in Figure 1, which documents the rate of discovery of Type I and Type III RM system specificities since the very first one was discovered and characterized in 1968 (8).

Bottom Line: REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems.All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly.Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing.

View Article: PubMed Central - PubMed

Affiliation: New England Biolabs, Ipswich, MA 01938, USA roberts@neb.com.

Show MeSH