Poly(dA:dT) tracts differentially modulate nucleosome remodeling activity of RSC and ISW1a complexes, exerting tract orientation-dependent and -independent effects

The establishment and maintenance of nucleosome-free regions (NFRs) are prominent processes within chromatin dynamics. Transcription factors, ATP-dependent chromatin remodeling complexes (CRCs) and DNA sequences are the main factors involved. In Saccharomyces cerevisiae, CRCs such as RSC contribute to chromatin opening at NFRs, while other complexes, including ISW1a, contribute to NFR shrinking. Regarding DNA sequences, growing evidence point to poly(dA:dT) tracts as playing a direct role in the active processes involved in nucleosome positioning dynamics. Intriguingly, poly(dA:dT) tract-containing NFRs span asymmetrically relative to the location of the tract, by a currently unknown mechanism. In order to get insight into the role of poly(dA:dT) tracts in nucleosome remodeling, we performed a systematic analysis of their influence on the activity of ISW1a and RSC complexes, with focus on their effect when located on linker DNA. Our findings revealed that poly(dA:dT) tracts differentially affect the activity of these CRCs. Moreover, we found differences between the effects exerted by the two alternative tract orientations. Our results support a model for the asymmetric chromatin opening that take place around these sequences.