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
The Functions of DNA Methylation by CcrM in Caulobacter Crescentus: A Global Approach
TL;DR: It is shown that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair, and that GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division.
Journal ArticleDOI
Going beyond five bases in DNA sequencing.
Jonas Korlach,Stephen Turner +1 more
TL;DR: In this opinion, several emerging single-molecule sequencing techniques that have the potential to directly detect many types of DNA modifications as an integral part of the sequencing protocol are highlighted.
Journal ArticleDOI
Deciphering bacterial epigenomes using modern sequencing technologies
TL;DR: Advances in DNA sequencing technology have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes.
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Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
Satoshi Hiraoka,Satoshi Hiraoka,Yusuke Okazaki,Mizue Anda,Atsushi Toyoda,Shin-ichi Nakano,Wataru Iwasaki +6 more
TL;DR: This study used single-molecule real-time and circular consensus sequencing techniques to reveal the ‘metaepigenomes’ of a microbial community in the largest lake in Japan, Lake Biwa, and revealed 22 methylated motifs, nine of which were novel.
Journal ArticleDOI
Metabolic and process engineering of Clostridium cellulovorans for biofuel production from cellulose.
TL;DR: This study is the first metabolic engineering of C. cellulovorans for n-butanol and ethanol production directly from cellulose with significant titers and yields, providing a promising consolidated bioprocessing (CBP) platform for biofuel production from cellulosic biomass.
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