Reb1 protein is an essential, auto-regulated DNA-binding protein that binds to many sites in the S. cerevisiae genome.
Recently we studied the detailed structures for a one-to-many example (namely, p53 using its disordered regions to bind to many partners), and we also studied the structures of a many-to-one example (namely, 14-3-3 usinglets single binding site to associate with many different disordered partners having different amino acid sequences).
Using histone modification signal to approximate nucleosome position, as in Kundaje et al. [ 7], we see that sites in every cluster have highly variable position of the signal maximum relative to the future GR binding site, that many sites demonstrate well-positioned and phased nucleosomes prior to GR binding, and that signal is again asymmetric.
At least for the repressor side of the equation, we see here that the demands for generating biochemical activity are lower than anticipated – our work challenges our colleagues in the field to determine the generality of previous assumptions, and measure the independent potential for many activators binding to "off target" sites.
Recently, it has been shown that FNR function is strongly inhibited by this kind of nucleoid-associated proteins, which block FNR access to many binding sites [ 20].
Reassuringly, our high-confidence peak calls include binding sites corresponding to many known target genes, including Pck1, Ppargc1a, and Crem (Additional file 1: Figure S3).
siRNA-mediated gene targeting experiments demonstrated that Doublesex, a transcription factor with consensus binding sites located adjacent to many dimorphically expressed transcripts that function in neural development, is required for regulation of sex-specific gene expression in the developing A. aegypti brain.
In addition to these binding sites, many other nucleotide sequences of the mRNAs are also homologous.
Reaplcement glu25GLY in the TF therefore acts as a permissive substitution for drift by the RE, allowing the DNA binding site to explore many new pathways including mutation to SREs while still maintaining an association with the TF.
In all, 44 intergenic HFR sequences were found to contain putative GAF binding sites, many with multiple instances or repetitions of the GAGAG motif.
