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In order to detect such events, we considered the set of Dichaete binding intervals in one species that do not overlap with any interval in a pairwise comparison with each other species, as well as the genes to which they are annotated.
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List of target genes annotated to Dichaete and SoxN DamID binding intervals in all species.
Given that Dichaete and SoxN binding intervals in known CRMs are preferentially conserved, indicating a link between functional binding and conservation, we asked whether they are also highly conserved at core intervals and direct target genes.
If a binding interval was identified at the same aligned position in an orthologous binding interval in more than one species, it was considered to be positionally conserved between those species.
I have logged helicopter flights that at times occur at two- to five-minute intervals in one hour's time.
De novo motif discovery was undertaken using MEME-ChIP searching the central 200 bases within each binding interval for either one or no motif per site between 6 and 30 bases in length [ 43].
In all cases, significantly more Sox motifs were found in Dichaete binding intervals than in control intervals (p < 4.03e-15, Wilcoxon rank sum test with continuity correction).
Performing the same analysis on the binding intervals identified in D. simulans reveals an even more striking effect, with 94.1% of commonly bound intervals showing binding conservation in D. melanogaster.
Not only were there a large number of binding intervals commonly bound in both species, intervals that are commonly bound in either species are significantly more likely to be conserved than intervals bound uniquely by one Sox protein.
Focusing on Dichaete binding intervals, we compared intervals that are bound in all four species, including D. pseudoobscura, to those that are unique to D. melanogaster.
Additional file 6: Enriched de novo motifs discovered in Sox binding intervals.
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