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Exact(5)
It is tempting to think that regional variation in chromatin structure creating more open or more closed chromatin is involved, as shown in yeasts [47], and also suggested by the differences of hotspot distribution in humans (reviewed in [48]) and mice [2], [49].
Intriguingly, the gene size appeared a major determinant, with larger active genes displaying more closed chromatin.
However, the average synonymous rate (dS) for genes in relatively open chromatin is higher than that for genes in a more closed chromatin structure.
Together, the 28 islands overlapped 20 markers found to be in a more closed chromatin state (log2 open < 0) and 26 markers in an open state (log2 open > 0).
Thus, the 4th chromosome data suggests that lower sequence coverage is associated with a more "closed" chromatin state in this largely heterochromatin chromosome.
Similar(54)
Besides, repressors are more associated with closed chromatin compared with activators.
Generally the role of the co-regulatory proteins is to recruit chromatin remodelling enzymes or chromatin-binding proteins in order to set up more open or closed chromatin configurations.
Another explanation could be that, as suggested by recent studies, HSCs and other stem cells have a more "open" chromatin structure to facilitate rapid gene transcription for multiple cell lineage differentiation programs with chromatin becoming more closed as differentiation occurs [13].
For example, a repressive mark can result in more closed (i.e. tightly packed) chromatin structure such that promiscuous binding by RNA polymerase is inhibited, thus reducing background expression.
However, comparing the strains under the same condition, the chromatin was always more closed in the xyr1 deletion strain compared to the wild-type strain (Fig. 2a, b) indicating a contribution of Xyr1 to a general (i.e. condition-independent) opening of chromatin in upstream regions of the cellulase-encoding genes.
If false positive hits were to be sampled from a very large promoter region (e.g. up to 5 kb upstream of TSS), the majority of the hits would not originate from the first 1 kb, where most true TFBSs are positioned, but from regions more upstream, where the chromatin structure is likely to be more closed.
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