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A stable ravine pattern at many 5′ promoters supports the emerging idea that it is crucial to examine non-promoter CpGs and CGIs in differential methylation analysis as non-promoter regions may have more dynamic methylation than 5′ promoter regions.
Taken together, the consistency of the ravine pattern, high DNase sensitivity and high associated gene expression, both across a variety of tissues and conditions suggests the genes associated with steep ravines are universally active in human cells.
Regarding the ravine pattern, we note that some degree of contrast between shores and CGIs is expected: the majority of CpGs are known to be methylated, with CGIs being the exception.
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Hansen et al. [ 38] and VanderKraats et al. [ 39] found tissue-specific ravine-like patterns emerging between cancer and healthy states as a differential methylation signature.
Although the association they saw was specifically in blood and limited to a family trio, it is further evidence that ravine-like patterns are positively correlated with gene expression.
The watershed (about 80 km2 in size) comprises a small mountainous valley with steep slopes and deep cut ravines, typical of the landscape pattern in high population intensity mid elevation zone of central Himalaya.
Another potentially relevant study showing a pattern similar to our ravines, from Wu et al. [ 41], found that the shores and shelves of unmethylated 5′ promoter CGIs, are associated with high Dnmt3a activity in the mouse genome.
The only locality at which we detected an effect of Opuntia was Ravine: the non-invaded site showed a disassortative pattern (R2 = 0.68, P = 0.003), whereas links were more homogeneous in the invaded site (R2 = 0.25, P = 0.12).
The centre of the city, with most of the administrative, cultural, and educational institutions, is laid out on a gridiron pattern that is broken only near the river by ravines in the steep bank.
Heavy with the loss of their firstborn and only child many years earlier, they seek to change the pattern of their lives in a context of icy ravines and wild silence.
Seasonally, three control patterns of travertine deposition rates were distinguished along the Ravine.
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