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Recently, a genome-wide analysis in mouse liver revealed several thousand CLOCK protein binding sites, most of which exhibited day-night variations in CLOCK occupancy, suggesting extensive and wide-reaching metabolic regulatory functions for CLOCK and other clock components.
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We can keep these running around the clock, with high-participation occupancy rates, so we're going to learn a whole new set of lessons we can add to our playbook".
Thus, USF1 binds to a majority of reference clock genes and its occupancy on these sites increases in the Clock Δ19 /Clock Δ19 mice.
DOI: http://dx.doi.org/10.7554/eLife.00426.011 To explore our observation that CLOCKΔ19 BMAL1 occupancy decreases in Clock Δ19 / Clock Δ19 mice we determined the relative affinity of CLOCK BMAL1, CLOCKΔ19 BMAL1 and USF1 complexes to E-boxes using EMSA.
In Clock Δ19 mutants, however, USF1 occupancy increases and CLOCKΔ19 occupancy decreases at these sites despite elevated CLOCKΔ19 mutant protein levels.
E-box occupancy demonstrated by CLOCK (top panels) and USF1 (bottom panels) is shown.
Thus, USF1 can suppress the Clock Δ19 mutant by increased occupancy of CLOCK BMAL1 E-box sites, acting as a partial agonist for CLOCK BMAL1-mediated transCLOCK BMAL1-mediated
Significant REV-ERBα occupancy was observed with the CLOCK gene, as diagrammed in Figure 1a.
The "pipeline occupancy" is given by running/total clocks required for one iteration.
Because USF1 and CLOCK BMAL1 compete for binding at the same E-boxes, and because CLOCKΔ19 BMAL1 exhibits a lower affinity for these sites, we predicted that there should be a global increase in USF1 occupancy at CLOCK BMAL1 binding sites in Clock Δ19 mutant mice.
Both SWI/SNF and Clock ATPase facilitate frq expression by generating a rhythm in nucleosome occupancy at the C-box (Cha et al. 2013; Wang et al. 2014).
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