Practice question

Scaffold Attachment Regions also termed Matrix Attachment Regions designate DNA elements anchoring loop domains to nuclear scaffold. Sequence analysis from multiple loci reveals enrichment for AT-rich stretches with topoisomerase II cleavage consensus, origin recognition elements and base unpairing regions possessing high untwisting potential under superhelical stress. AT-richness favors minor groove interaction with scaffold proteins and propensity to become single stranded, facilitating protein binding. GC-rich islands associate with active promoters, CpG islands regulate imprinting, rRNA gene clusters localize to nucleolus not scaffold attachment. Therefore SARs characteristic AT-rich nature explains high scaffold affinity.