Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through 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 ∼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 hypo-methylated 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. [Display omitted] •ALaP-seq to profile PML body-associated regions•PML bodies frequently associate with Yp locus to regulate Y-linked genes•PML bodies exclude DNMT3A to maintain hypo-methylated state of associated promoters Kurihara et al. determined genetic loci associated with PML bodies in mouse ESCs by developing APEX-mediated chromatin labeling and purification (ALaP). PML bodies frequently associate with the short arm of the Y chromosome to regulate clustered Y-linked genes by maintaining hypo-methylated DNA through excluding DNMT3A.