Sub-nuclear transcription factor targeting remodels heterochromatin to activate compartmentalized gene programs [ATAC, Cut & Tag]

Sub-nuclear localization of heterochromatin enables stable lineage-specific gene repression. The mechanisms by which pioneer transcription factors (TFs) access these loci to selectively activate lineage-specific genes remain poorly understood. Here, using a model of TF-induced cardiac reprogramming, we show that Hand2’s ability to reprogram cells requires its selective compartmentalization within perinucleolar heterochromatin wherein many key target genes reside. We identify the nucleolar targeting region of Hand2, which is mechanistically separable from DNA-binding. Using a series of separation of function mutants, we find that compartmentalization creates high local concentrations of Hand2 homodimers required for binding of suboptimal DNA motifs within lineage-specific gene enhancers. Altogether, our results establish a causal relationship between TF sub-nuclear localization and selective activation of lineage-specific gene programs. Thus, our data support the notion that lineage-specific programs are functionally compartmentalized within the nucleus, and we provide a mechanistic model by which TF sub-nuclear localization orchestrates selective activation of lineage specific genes. To investigate the impact of sub-nuclear localization of Hand2 on gene expression we profiled reprogramming experiments expressing different separation of function mutants via ChIP-seq and RNA-seq