Positive and Negative Design for Nonconsensus Protein-DNA Binding Affinity in the Vicinity of Functional Binding Sites

Abstract

Recent experiments provide an unprecedented view of protein-DNA binding in yeast and human genomes at single-nucleotide resolution. These measurements, performed over large cell populations, show quite generally that sequence-specific transcription regulators with well-defined protein-DNA consensus motifs bind only a fraction among all consensus motifs present in the genome. Alternatively, proteins in vivo often bind DNA regions lacking known consensus sequences. The rules determining whether a consensus motif is functional remain incompletely understood. Here we predict that genomic background surrounding specific protein-DNA binding motifs statistically modulates the binding of sequence-specific transcription regulators to these motifs. In particular, we show that nonconsensus protein-DNA binding in yeast is statistically enhanced, on average, around functional Reb1 motifs that are bound as compared to nonfunctional Reb1 motifs that are unbound. The landscape of nonconsensus protein-DNA binding around functional CTCF motifs in human demonstrates a more complex behavior. In particular, human genomic regions characterized by the highest CTCF occupancy, show statistically reduced level of nonconsensus protein-DNA binding. Our findings suggest that nonconsensus protein-DNA binding is fine-tuned around functional binding sites using a variety of design strategies.

Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences

“…We thus investigated the sequence context effect on RNAP pausing between the true and false PIEs. As described below and in our previous studies (24)(25)(26)(27)(28)(29), we have previously revealed that nonconsensus repetitive DNA sequence elements in the vicinity of a consensus protein-binding motif statistically enhance the protein binding to its "site." This finding led us to hypothesize that a similar context effect could provide the mechanism responsible for the genome-wide regulation of RNAP pausing at PIE motifs.…”

“…2A (also refs. 26,27). Then, we computed the average free energy difference between the two groups comprising each randomized group pair (i), (ii), and (iii), respectively.…”

“…We have characterized the mechanism of this context effect (24)(25)(26)(27)(28)(29) as an extension of the concept for nonspecific protein-DNA binding introduced by von Hippel and coworkers (30)(31)(32)(33) 40 y ago. Briefly, nonspecific protein-DNA binding (i.e., protein sliding on DNA) represents an electrostatically dominated mechanism, and it was usually assumed that it is uniform (on average) and entirely nonspecific outside of short specific recognition motifs along the genomic DNA (33).…”

“…experimental knowledge of protein-DNA binding affinity; rather, it uses DNA sequences as the only input (24)(25)(26)(27)29). Briefly, nonspecific DNA sequences enriched in certain repetitive sequence patterns such as homo-oligonucleotide tracts can modulate the spectrum of protein-DNA binding energy fluctuations (24,28).…”

The Determinants of Directionality in Transcriptional Initiation

“…Non-consensus binding of PIC components to the NDR has been suggested to explain binding of general TFs to promoter regions without any discernable recognition sequences [42]. Such binding was promoted by the TF Reb1 in yeast and inhibited by CTCF in human cells [43]. NDRs with two PICs are further characterized by a greater occupancy of the − 1 nucleosome [43], suggesting that the chromatin structure at the NDR promotes opening of a transcription bubble and is conducive to bidirectional transcription, with PICs forming in both directions at the edges of the flanking nucleosomes.…”