REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
TLDR
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems that contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data.Abstract:
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. 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. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.read more
Citations
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Journal ArticleDOI
Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution
Yimeng Kong,Lei Cao,Gintaras Deikus,Yu Fan,Edward A. Mead,Weiyi Lai,Yizhou Zhang,Raymund L. Yong,Robert Sebra,Hailin Wang,Xue-Song Zhang,Gang Fang +11 more
TL;DR: A metagenomic method to quantitatively deconvolve 6mA events from a genomic DNA sample into species of interest, genomic regions, and sources of contamination is developed and it is found that bacterial contamination explains the vast majority of 6mA in DNA samples from insects and plants.
Journal ArticleDOI
The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
Iratxe Estibariz,Annemarie Overmann,Florent Ailloud,Florent Ailloud,Juliane Krebes,Christine Josenhans,Christine Josenhans,Sebastian Suerbaum,Sebastian Suerbaum +8 more
TL;DR: In this article, a highly conserved GCGC-specific m5C MTase (JHP1050) was found to be active in all of 459 H. pylori genome sequences analyzed.
Journal ArticleDOI
Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria
Pedro H. Oliveira,Gang Fang +1 more
TL;DR: It is proposed that highly conserved DNA methyltransferases (MTases) represent a unique opportunity for bacterial epigenomic studies and how these MTases may emerge as promising targets for the development of novel epigenetic inhibitors for biomedical applications is discussed.
Journal ArticleDOI
Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.
Daehwan Chung,Daehwan Chung,Jennifer R. Huddleston,Jennifer R. Huddleston,Joel Farkas,Joel Farkas,Janet Westpheling,Janet Westpheling +7 more
TL;DR: Preliminary analysis of other Caldicellulosiruptor species suggested that this restriction/modification activity is widespread in this genus, and a phylogenetic analysis based on sequence alignment and conserved motif searches identified features of C beI distinct from other members of this group and classified CbeI as a member of a novel subfamily of HaeIII-like enzymes.
Journal ArticleDOI
Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis.
Ying-Yee Kong,Jennifer Ma,Keisha Warren,Raymond S. W. Tsang,Donald E. Low,Donald E. Low,Frances B. Jamieson,Frances B. Jamieson,David C. Alexander,David C. Alexander,Weilong Hao +10 more
TL;DR: Recombination was found in genes associated with virulence factors, antigenic outer membrane proteins, and vaccine targets, suggesting an important role of homologous recombination in rapidly altering the pathogenicity and antigenicity of Neisseria meningitidis.
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