Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice

Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice. [Display omitted] •A conserved antisense promoter is located within each of the Pcdhα alternate exons•Antisense lncRNA transcription leads to DNA demethylation of promoters and CBSs•CTCF/cohesin drive the assembly of Pcdhα enhancer/promoter complex via loop extrusion•Coupling lncRNA transcription to DNA demethylation ensures stochastic promoter choice Coupling transcription of a long noncoding RNA to DNA demethylation ensures stochastic promoter choice for clustered Protocadherin α genes, which is essential for the establishment of a neuronal surface identity code involved in circuit assembly.