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These phage binders likely bind at the DNase I: actin interface.
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Some TFs can bind to the DNase I-resistant regions with high in vivo nucleosome occupancy and might regulate gene expression in a cell-type-specific way.
LARC binds to the DNase hypersensitive 2 site in the human β-globin locus control region (LCR) and transactivates β-like globin genes [ 30].
As a negative control, no complex formation was observed using Gc-globulin, which binds the DNase-actin complex through actin [ 20].
After 10 min equilibration at 37 °C, the DNase I was added to yield a final DNase I concentration of 2 U/L.
Subsequently, the entire reaction contents were transferred to 110 μL of Zymo DNA Binding Buffer to inactivate the DNase.
Then, more transcription factors tend to bind onto the opening site and the DNase I hypersensitive site is created.
We have known that transcription factors tended to bind to DNase I hypersensitive sites; thus we combined the DNase I hypersensitive sites with promoter regions to construct a new model.
Such DNase footprints are the actual locations where the TF binds and are therefore protected from DNase cleavage within the DNase HS site.
Also, the DNase 1 accessibility at TSSs directly correlated with increasing transcriptional activity.
Notably, there is a dip in the H3K27ac signal in the center of the DNase peak summit, which is a reflection of bound TFs that can displace histones.
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