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At present, several classes of histone modifications and their respective enzymatic modification systems have been identified (Table 1) [ 26].
Putative restriction modification systems have been identified using the Restriction-ModificationFinder-1.0 server (https://cge.cbs.dtu.dk/services/Restriction-ModificationFinder-1.0/) based on the Restriction Enzyme database (REBASE, http://rebase.neb.com/rebase/rebase.html) [ 56].
Genes encoding restriction modification systems have previously been observed in this location in both S. aureus and S. epidermidis (Mongkolrattanothai et al. 2004; Gill et al. 2005; Noto et al. 2008).
At present several classes of histone modifications and their respective enzymatic modification systems have been identified [ 72, 75] and amongst their epigenetic substrate marks, lysine and arginine modifications are probably the best studied: acetylation and methylation of lysine residues, as well as methylation of arginine [ 72, 75, 76].
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Genes that encode these different components of the protein modification system have been reported to be associated with SLE.
In addition, restriction-modification systems have been discovered in Thermotoga, for instance, we have recently characterized a Thermotoga-specific Type II restriction-modification system [ 23].
Restriction-modification systems have been postulated to be one of the key elements that prevent foreign DNA integration into the host genome by degradation of DNA that is not methylated by the R-M system's modification enzyme.
Two novel cases of sequence permutation in DNA MTases implicated in restriction-modification systems have been identified, which suggest that members of the δ and ζ classes (M. MwoI and M. TvoORF1413P, respectively) evolved from β-class MTases.
These results pointed out that the hypusine modification system has pleiotropic effects and can act either as promoter or suppressor of malignant transformation, depending on the cellular environment.
Similar to S. mansoni, it is likely that 5mC detected in mixed-sex adult S. japonicum and S. haematobium samples is preferentially associated with females where this DNA modification system has previously been shown to regulate oviposition [ 13].
Potential mobility of restriction-modification systems has been suggested by evolutionary/bioinformatic analysis of prokaryotic genomes.
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