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Official websites use. Share sensitive information only on official, secure websites. Corresponding authors: R. DNA sequence is a major determinant of the binding specificity of transcription factors TFs for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with highly similar DNA binding motifs but distinct in vivo targets. Currently, it is not well understood how TFs with seemingly identical DNA motifs achieve unique specificities in vivo.
Here, we used custom protein binding microarrays to analyze TF specificity for putative binding sites in their genomic sequence context. Computational analyses suggest that nucleotides outside E-box binding sites contribute to specificity by influencing the 3D structure of DNA binding sites. Thus, local shape of target sites might play a widespread role in achieving regulatory specificity within TF families. Transcriptional regulation is effected primarily by sequence-specific transcription factors TFs that recognize short DNA sequences 5โ15 base pairs long in the promoters or enhancers of the genes whose expression they regulate Bulyk, Determination of the DNA recognition properties of TFs is essential for understanding how these proteins achieve their unique regulatory roles in the cell.
TFs are typically annotated according to the structural class of their DNA binding domains. Members of a particular class i. However, despite apparently shared binding specificities, individual TF family members often exhibit non-redundant functions. In some cases, differences in the core DNA binding site motifs have been shown to contribute to differential in vivo binding by closely related TFs Busser et al. However, in many cases the DNA motifs of paralogous TFs are virtually identical, and still the proteins select different genomic targets in vivo.
In these cases, interactions with protein cofactors are thought to be responsible for differential in vivo DNA binding of paralogous TFs. However, such cofactors can be difficult to identify and only a few conclusive examples are known e.
Another factor that determines in vivo TF binding is the local chromatin environment Arvey et al. Nevertheless, protein cofactors and chromatin context are unlikely to completely explain differential binding specificity of paralogous TFs. Here, we investigate a potential mechanism through which TFs with highly similar DNA binding motifs can achieve differential binding in vivo. Several studies have indicated that nucleotides flanking TF binding sites i.