Nucleation of DNA Repair Factors by FOXA1 Links DNA Demethylation to Transcriptional Pioneering

We report that the winged helix transcription factor FOXA1 is unexpectedly associated with components of single and double stranded-DNA repair complexes. Biochemical studies and high-throughput approaches validated the hierarchical composition of this FOXA1-nucleated machinery and revealed the dependency on FOXA1 for global targeting of the key repair polymerase POLB. Genome-wide DNA methylomes at single-base resolution demonstrated that FOXA1-DNA repair complex is functionally linked to DNA demethylation in a lineage specific fashion. Loss-of-function studies indicate that a significant portion of FOXA1-bound regions display localized reestablishment of methylation and that the subsets with most consistent hypermethylation are represented by active promoters and enhancers that also exhibit the greatest depletion of POLB following FOXA1 removal. Consistently, forced expression of FOXA1 commits its binding sites to an active DNA demethylation in a POLB dependent manner. Finally, we showed that FOXA1-associated DNA demethylation is tightly coupled with genomic targeting of estrogen receptor and estrogen responsiveness. Together, our results link FOXA1-associated DNA demethylation to its transcriptional pioneering.

本研究报道，翼螺旋转录因子（winged helix transcription factor）叉头框A1（FOXA1）与单链及双链DNA修复复合物组分存在意外关联。生化研究与高通量实验手段验证了该FOXA1成核复合物的分级组装模式，并揭示关键修复聚合酶DNA聚合酶β（POLB）的全基因组靶向依赖于FOXA1。单碱基分辨率全基因组DNA甲基化组分析表明，FOXA1-DNA修复复合物以谱系特异性方式与DNA去甲基化存在功能关联。功能丧失实验显示，FOXA1结合区域中有显著比例发生局部甲基化重建；其中高甲基化程度最稳定的亚群对应活性启动子与增强子，此类区域在FOXA1敲除后同样呈现出POLB的最大程度耗竭。与之相符的是，强制过表达FOXA1可使其结合位点以POLB依赖的方式介导主动DNA去甲基化。最后，本研究证实FOXA1相关的DNA去甲基化与雌激素受体的基因组靶向及雌激素应答紧密耦合。综上，本研究结果将FOXA1相关的DNA去甲基化与其转录先驱活性建立了关联。