Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.

The 9p21 locus encodes critical cell cycle regulators p16, p14, and p15 and contains a high density of SNPs associated with aging-related diseases. Progress toward understanding 9p21 regulatory mechanisms has been constrained by complex transcript structures and a shortage of cell models that retain physiologic locus control. We innovated tools to deconvolve the expression and regulation of 9p21 transcripts in single cells. We find that 9p21 transcripts exhibit highly divergent expression across tissues and cell types, with p15 predominating. Despite being frequently conflated under the term CDKN2A, p14 and p16 are independently expressed across tissues, cell types, aging, and in a fibroblast model of replicative senescence. We annotate a network of cis-regulatory elements (CREs), whose activities and interactions underpin these complex regulatory dynamics. Our systematic characterization of 9p21 transcripts and CREs provides mechanistic insights and the tools for future studies of this vital locus.