In this study, using highly quantitative methylation analysis of individual LINE-1 repeats, we showed that methylation is not the same in all individuals and that it does not have the same levels on all loci even when comparing the same category of loci (autosomal or X-linked).
In agreement with previous genome-wide studies, there are three distinct categories of loci.
Variability was determined across the total dataset, and was also analysed following subdivision into five categories of loci: cytochrome p450 mono-oxygenases; glutathione-S-transferases; carboxy/cholinesterases; other detoxification loci; and other loci with no known detoxification function.
Here, we provide an examination of the evolution of promoter regions in the different lineages pertaining to the two subspecies SD, as well as S. pyogenes, and assess whether different rates of evolution are associated with different metabolic functions or biochemical categories of loci.
In each of these "HAT-acetylation mark" comparisons, variations in acetylation levels between different categories of loci can be observed, but with the same patterns for all the residues tested (except for histone H2AK5ac, H3K14ac and H3K23ac for which the antibodies used in the ChIP may have been too weak for the analysis).
To control for other factors that may affect this conservation score, we included three other covariates: the motif type of each locus, the length in the human genome, and the functional category of each locus (coding, 5′-UTR, etc).
The scale determines which category of health locus of control – internal, chance or powerful others – a patient most identifies with.
In studies estimating pairwise categories of relatedness, the class of loci most commonly used have been short tandem repeats (STRs), but the use of SNPs has been increasing (Weir et al. 2006).
In the category of the NC loci, two loci, ymdA and c1602 (predicted proteins) were downregulated in REL606 and CVE2, in the exponential phase.
We define three categories of trivial locus topologies (Fig. 1): chains, forks and bubbles, which if isolated from any other branching point, are straightforward to resolve.
