The proximal sites had higher upstream nucleosome occupancy than downstream nucleosome occupancy.
High-usage proximal sites had higher upstream nucleosome occupancy and lower downstream nucleosome occupancy.
Furthermore, one of the most significant findings in our study is that compared with the low-usage proximal sites, the high-usage proximal sites had a higher upstream nucleosome occupancy (p < 1 × 10-11, Figure 4A).
Proximal polyadenylation sites have an adjustable upstream nucleosome occupancy, which correlates with the site usage, and may signal to RNA polymerase II to slow down and prepare for a 3′ end processing event.
For this reason, we calculated 5′ leader ribosome density (5′RD) for each gene expressed during the IDC, defined as upstream ribosome occupancy normalized for mRNA expression level and size of the leader sequence (5′ leader ribosome footprint rpkM/5′ leader mRNA rpkM).
In this strategy, real-time occupancy upstream of the on-ramp is used in order to determine the metering rate for the next cycle.
In contrast, the active variant H2A.Z had high occupancy upstream and decreasing presence downstream.
For example, the scatter plot for one of these families, tProUGG with 10 isogenes present on different chromosomes and Pearson correlation of −0.6544, shows greater enrichment of pol III near TSS of isogenes and lower nucleosome occupancy upstream.
EDTA treatment of BG3 cells increased multiple E spl -C transcripts a hundrE spl -Cor more, and NICD occupancy upstranscriptsHmβ and HLHm3 increased to 10-fold and 6-fold enrichment.
Caveolin-1 was strongly responsive in several organs, and the HRE pair in its upstream region showed increased occupancy by glucocorticoid receptor in response to corticosterone.
