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Specific modified sites were identified via LC-MS/MS analysis of digested histone H4.
The sequence comparison showed that the selection force has limited the divergence in the regions flanking the domains of PL10 related genes in fish, frog, bird and mammals, and most of the epigenetically modified sites were highly conserved among these species.
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Besides all four histones (H2A, H2B, H3, and H4) can be O-GlcNAcylated by OGT (Zhang et al., 2011; Sakabe et al., 2010) (Table 1), the accurate modified sites are also identified gradually.
The amino acids around the modified sites are not obviously conserved, a slight difference between the preferences of amino acids for the ubiquitylation and non-ubiquitylation sites.
All of the modified sites are asparagine residues, in all except one case in the conventional consensus sequence of N-linked glycans, namely Asn-X-Ser/Thr.
Injection in Xenopus laevis oocytes of regionally methylated plasmids has shown that a few methylated cytosines can inhibit a flanking promoter but a threshold of modified sites is required to organize a stable, diffusible chromatin structure.
It is possible that the modified sites are particularly prone to photo-crosslinking.
The notion that the modified sites are more prevalent in mitotic compared to postmitotic tissues, such as brain and heart muscle, further favors a functional role of these sites.
In monomethylation of H3 lysine 4 (H3K4me1) and trimethylation of H3 lysine 36 (H3K36me3), the entropies in hyper-modified sites were significantly higher than those in hypo-modified sites (P < 1.3e-7 from Wilcoxon test).
Modified site is the position of the initial and final amino acids of peptide in the protein sequence.
Type IIM sites were considered separately because Type IIM REases cleave only modified sites and are comparable to Type IV REases in that regard [ 5].
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