However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements.
Among these, the so-called HAR (human accelerated regions) or haCNS (human accelerated conserved non coding sequences) elements are highly conserved non-coding regions that have changed rapidly along the human lineage and are thought to correspond mainly to regulatory elements that could contribute to species-specific transcriptional programs [18], [19], [22], [23].
Since the TUs of protein coding genes are largely composed of introns (in terms of sequence length), this suggests that FOXL2 acts mainly through intronic regulatory elements (as previously described for Fst) (Blount et al., 2009).
We first specified the regions extending 30 kb on each side of interested genes and used the estimated CN values of 1 kb non-overlapping windows in each individual for post-analysis, mainly considering that the regulatory elements may be included in the upstream or downstream of a gene.
Almost 6000 SOX10-occupied sites were detected, but unlike MITF they were mainly located at distal regulatory elements with only around 80 sites at the proximal promoter.. SOX10 recognition motifs were strongly enriched at SOX10 bound sites some of which were organised as degenerate palindromes.
An extremely important question thus arises – that is, 'what mechanism(s) is (are) responsible for favouring the mutated P53 mRNA over the wild-type ones?' A methylation of DNA regulatory elements – mainly promoters, is one of the mechanisms of tumour suppressor genes silencing (Watanabe et al, 2007).
Combined with the observation that TADs are functional domains for enhancer action, it has been proposed that looping interactions between genes and distal regulatory elements occur mainly within TADs (e.g., [ 6, 70, 71, 97]).
Since we were mainly interested in highly conserved regulatory elements, we demanded an average similarity level at least as high as the average exon conservation between the species under comparison.
CTCF may act as an insulator, mainly by inhibiting inappropriate interactions between regulatory elements on adjacent or distal chromatin domains.
Starting from all published tardigrade sequences as well as 607 unpublished new sequences from Milnesium tardigradum, we analyse tardigrade specific clusters of related proteins, functional protein clusters and conserved regulatory elements in mRNA mainly involved in mRNA stability.
