Reactivation of fetal hemoglobin expression by the downregulation of BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding of BCL11A-mediated repression of γ-globin gene (HBG1/2) transcription is lacking, as studies to date used perturbations by shRNA or CRISPR-Cas9 gene editing. We leveraged the dTAG PROTAC degradation platform to acutely deplete BCL11A protein in erythroid cells and examined consequences by nascent transcriptomics, proteomics, chromatin accessibility, and histone profiling. Among 31 genes repressed by BCL11A, HBG1/2 and HBZ show the most abundant and progressive changes in transcription and chromatin accessibility upon BCL11A loss. Transcriptional changes at HBG1/2 were detected in <2 h. Robust HBG1/2 reactivation upon acute BCL11A depletion occurred without the loss of promoter 5-methylcytosine (5mC). Using targeted protein degradation, we establish a hierarchy of gene reactivation at BCL11A targets, in which nascent transcription is followed by increased chromatin accessibility, and both are uncoupled from promoter DNA methylation at the HBG1/2 loci.

通过下调 BCL11A 重新激活胎儿血红蛋白表达是治疗 β-血红蛋白病的一种有前景的方法。由于迄今为止的研究使用了 shRNA 或 CRISPR-Cas9 基因编辑的扰动，因此缺乏对BCL11A 介导的 γ 球蛋白基因 ( HBG1/2 ) 转录抑制的详细了解。我们利用 dTAG PROTAC 降解平台来急剧消耗红系细胞中的 BCL11A 蛋白，并通过新生转录组学、蛋白质组学、染色质可及性和组蛋白分析来检查后果。在 BCL11A 抑制的 31 个基因中，HBG1/2和HBZ在 BCL11A 缺失后在转录和染色质可及性方面显示出最丰富且渐进的变化。HBG1/2的转录变化在 <2 小时内即可检测到。急性BCL11A 耗竭后，HBG1/2会重新激活，而启动子 5-甲基胞嘧啶 (5mC) 不会丢失。利用靶向蛋白质降解，我们在 BCL11A 靶标处建立了基因重新激活的层次结构，其中新生转录之后是染色质可及性增加，并且两者都与 HBG1/2 位点的启动子 DNA 甲基化解偶联。