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The START domain of 54kDa endosomal StarD3 (MLN64) is an helix grip fold, providing a hydrophobic binding site for one molecule of cholesterol, facilitating cholesterol trafficking to the endoplasmic reticulum (ER), mitochondria and plasma membrane (Charman et al., 2010; Alpy et al., 2013; van der Kant et al., 2013).
The analysis of the ASRAH domain presented here identifies the binding site for one more of these β-sandwich scaffolds.
For most of predicted binding sites there is more than one predicted miRNA (cooperativity), and this is further attenuated by more than one binding site for one miRNA (multiplicity).
This means that over-representation of a certain binding site for one transcription factor in a gene promoter region may not always predict the binding of the exact same factor.
Furthermore, Krebs et al. could drive the demethylation of an artificial island with an intermediate CpG density by inserting a binding site for one such transcription factor (called REST) into it.
Then, if a binding site for one of four common transcription factors (nuclear respiratory factor 2 (NRF), GC boxes (GC), Yin and Yang 1 (YY), and activator protein 1 (AP)) was found, a value of 0.1 was subtracted.
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Cis-regulatory modules (CRMs, also called enhancers) are approximately 1-kb long sequences that typically harbor multiple binding sites for one or more TFs and mediate the combinatorial influence of those TFs on gene expression (Davidson 2010).
Compatibility between CRMs could then be viewed as compatibility between binding sites for one or more transvection-mediating factors.
Twenty-nine RP genes had binding sites for three transcription factors, 22 had binding sites for two, and 19 had binding sites for one (Fig. 2).
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context the cells used in the experiment.
It is possible that there are multiple copies of the oligo binding sites for one of these assays in the D. serrata genome.
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