Genomic profiling of PML bodies by ALaP-seq reveals transcriptional regulation by PML bodies through the DNMT3A exclusion

The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with an ~300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body-association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypomethylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D-nuclear space and provides insights into the functional properties of nuclear structures for genome function.早幼粒细胞白血病（PML）小体是一类与染色质物理结合的相分离核结构，提示其在基因组功能中发挥关键作用。然而，其在转录调控中的功能尚不清楚。我们开发了APEX介导的染色质标记与纯化（APEX-mediated chromatin labeling and purification，ALaP）技术，用以鉴定与PML小体邻近的基因组区域。研究发现，在小鼠胚胎干细胞中，PML小体可与全基因组范围内的活性调控区域，以及Y染色体短臂约300kb的区域（YS300）发生关联。PML小体与YS300的关联，对于邻近的Y连锁成簇基因的转录活性至关重要。从机制层面来看，PML小体构建出从头DNA甲基转移酶DNMT3A无法进入的特异性核空间，从而稳定维持了Y连锁基因启动子区域的低甲基化状态。本研究阐明了三维核空间中基因调控的全新机制，为解析核结构的基因组功能属性提供了重要见解。