DNA bendability and nucleosome positioning in transcriptional regulation

Abstract The placement of nucleosomes along genomic DNA is determined by signals that can be specific or degenerate at the level of sequence; the latter signals are harder to find using conventional methods. In recent years, the development of sophisticated machine learning techniques that can extract subtle phased signals has improved our ability to distinguish between various classes of nucleosome-positioning sequences. Our knowledge of the structural mechanics of free DNA also has reached the point where it can be fruitfully incorporated into predictive models. More importantly, the accumulation of high-resolution structures with proteins bound to DNA, and those of nucleosomes in particular, has provided important clues about the role of DNA bending and flexibility in nucleosome positioning