Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion

Mol Cell. 2020 May 7;78(3):493-505.e8. doi: 10.1016/j.molcel.2020.04.004. Epub 2020 Apr 29.


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.

Keywords: APEX; DNA methylation; PML; Y chromosome; chromatin; phase separation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Chromatin / genetics
  • Chromatin / metabolism
  • DEAD-box RNA Helicases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA Methylation
  • DNA Methyltransferase 3A
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / genetics
  • Embryonic Stem Cells / physiology
  • Endonucleases / genetics
  • Gene Expression Regulation*
  • High-Throughput Nucleotide Sequencing
  • Intranuclear Inclusion Bodies / genetics*
  • Intranuclear Inclusion Bodies / metabolism
  • Mice, Knockout
  • Minor Histocompatibility Antigens / genetics
  • Multifunctional Enzymes / genetics
  • Multigene Family
  • Oxidative Stress
  • Promyelocytic Leukemia Protein / genetics
  • Promyelocytic Leukemia Protein / metabolism
  • Proteins / genetics
  • Transcription Factors / genetics
  • Y Chromosome / genetics*
  • Y Chromosome / metabolism


  • Chromatin
  • Dnmt3a protein, mouse
  • Eif2s3y protein, mouse
  • Minor Histocompatibility Antigens
  • Multifunctional Enzymes
  • Pml protein, mouse
  • Promyelocytic Leukemia Protein
  • Proteins
  • Transcription Factors
  • Uty protein, mouse
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A
  • Apex2 protein, mouse
  • Endonucleases
  • Ddx3y protein, mouse
  • DEAD-box RNA Helicases
  • DNA-(Apurinic or Apyrimidinic Site) Lyase