Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions

Abstract

S/MARs are DNA elements 300 to several thousand base-pairs long, which are operationally defined by their affinity for the nuclear scaffold or matrix. S/MARs occur exclusively in eukaryotic genomes, where they mediate several functions. Because S/MARs do not have a clearcut consensus sequence, the characteristics that define their activity are thought to be structural. Ubiquitous S/MAR binding proteins have been identified, but to date no unique binding sequence or structural motif has been found. Here we show by computational analysis that S/MARs conform to a specific design whose essential attribute is the presence of stress-induced base-unpairing regions (BURs). Stress-induced destabilization (SIDD) profiles are calculated using a previously developed statistical mechanical procedure in which the superhelical deformation is partitioned between strand separation, twisting within denatured regions, and residual superhelicity. The results of these calculations show that BURs exhibit a succession of evenly spaced destabilized sites that would render part or all of the S/MAR sequence single stranded at sufficient superhelicity. These analyses are performed for a range of sequenced S/MAR elements from the borders of eukaryotic gene domains, from centromeres, and from positions where S/MARs are known to support the action of an enhancer. The results reported here are in excellent agreement with earlier in vitro chemical reactivity studies. This approach demonstrates the potential for computational analysis to predict the points of division of the eukaryotic genome into functional units (domains), and also to locate certain cis-regulatory sequences.