DNA structural and sequence determinants for nucleosome positioning

Positioned nucleosomes are thought to be regulators of genome function but the role of DNA sequence and structure in the control of positioning is poorly understood. We examined the intrinsic curvature of DNA sequences that are known to position histone octamers at single translational sites as a first step to investigate this problem and discovered a conserved pattern of intrinsic DNA curvature that was proposed to direct the formation of nucleosomes to unique positions. The pattern consists of two 50-60 base pair regions of curved DNA separated by preferred lengths of non-curved DNA. The conserved pattern was also seen in all 57 satellite sequences present in the GeneBank database and the distances between successive pairs of curved elements in repeated arrays of satellite monomers were similar to the average spacing of nucleosomes in chromatin. To test the significance of the pattern, ten synthetic DNAs were constructed which contain two regions of curved DNA that are separated by non-curved regions of variable length. Translational mapping of in vitro reconstituted nucleosomes demonstrated that two of the fragments positioned nucleosomes at a single site while most of the remaining fragments positioned octamers at multiple sites spaced at 10 base intervals. In support of the curvaturebased model, the positioning sequences contained non-curved central regions of the same lengths that were seen in natural positioning sequences and displayed an affinity for histone octamers comparable to the strongest known natural positioning sequences.