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 highly heterogeneous methylated genomes and diverse restriction-modification systems of bloom-forming Microcystis.
TL;DR: Genomic comparisons reveal that methyltransferases (some partial) may have been acquired from the environment through horizontal gene transfer.
Journal ArticleDOI
Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078
Katherine R. Hargreaves,Katherine R. Hargreaves,Anisha M. Thanki,Bethany R. Jose,Marco R. Oggioni,Martha R. J. Clokie +5 more
TL;DR: These findings show key differences between the two strains in terms of their genetic capacity for MGE transfer, including the carriage of horizontally transferred genes appear to have genome wide effects based on two different methylation patterns.
Journal ArticleDOI
Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA
TL;DR: In eukaryotes, N4CMT deposits 4mC at active transposons and certain tandem repeats, and fusion to a chromodomain shapes its "histone-read-DNA-write" architecture recognizing silent chromatin marks as discussed by the authors .
Journal ArticleDOI
Functional characterization of the type II PamI restriction-modification system derived from plasmid pAMI7 of Paracoccus aminophilus JCM 7686
TL;DR: The PamI system can stabilize plasmid pAMI7 in a bacterial population, most probably at the postsegregational level, which indicates the crucial role of the analyzed R-M system in the stable maintenance of pAMI 7, which is, to the authors' knowledge, the first report of 'symbiosis' between a R-m system and a plasmids in the Alphaproteobacteria.
Journal ArticleDOI
Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and Other Coronaviruses: A Genome-wide Comparative Annotation and Analysis.
Mohammed Tarique,Shaban Ahmad,Arshi Malik,Irfan Ahmad,Mohd Saeed,Ahmad Almatroudi,Talal Qadah,Manal Abdulaziz Murad,Mutaib M Mashraqi,Qamre Alam,Yousef Al-Saleh +10 more
TL;DR: In this paper, the authors have analyzed the whole genomes of different coronaviruses infecting humans and animals in different geographical locations around the world and identified the similarity and the mutational adaptation of the coronavirus from different host and geographical locations to the SARS-CoV2.
References
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