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For example, in a mammalian genome, there are about 10,000 binding regions for a TF.
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In living cells, growing microtubule plus ends provide a transient binding region for a large number of plus-end tracking proteins (+TIPs) that either regulate microtubule dynamics or mediate interactions with other cellular substructures such as the plasma membrane, organelles, or kinetochores of chromosomes in mitosis.
In an alternative analysis, we screened the center of the PPARγ and RXR monosites and PPARγmoPET2+/RXR binding regions for the frequency of occurrence of a reported PPARγ/RXR binding motif using previously described PWMs [15], [30], [31].
Comparing the expression profiling data with the ChIP-seq data, we identified a total of 727 genes (937 AR binding regions) for which the genes were changed by two fold in the ETOH vs. Mock comparison; among them, 543 genes (716 AR binding regions) were down regulated, and 184 genes (221AR binding regions) were up-regulated.
The deleted peptide in NS3 causes the loss of binding regions for the protein kinase R, cleavage and polyadenylation specificity factor, as well as a nuclear export sequence.
Docking simulations identified two binding regions for Ole within the integrase active site.
Computational modeling of MIF and RTL1000 binding interactions with CD74 predicted the presence of three CD74 binding regions for each MIF homotrimer.
We also identify key amino acids in the DC-SIGN carbohydrate recognition domain that are required for HHV-8 infection and compare these results with published binding regions for ICAM-2/3 and HIV-1 gp120.
The objective of this work is to understand the nature (i.e. size and properties) of preferred protein-ligand binding regions for large, multi-domain molecules such as antibodies.
Ji et al. recently showed that ChIP-seq has better ability than ChIP-Chip in identifying TF binding regions for NRSF [24].
We have found the binding regions for both fibronectin and fibrinogen in LigB to overlap within repeats 9 to 11, with repeats 9 and 10 binding directly and repeat 11 acting as an enhancer (Table 2).
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