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

Misuzu Kurihara; Kagayaki Kato; Chiaki Sanbo; Shuji Shigenobu; Yasuyuki Ohkawa; Takeshi Fuchigami; Yusuke Miyanari

doi:10.1016/j.molcel.2020.04.004

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.

Authors

Misuzu Kurihara¹, Kagayaki Kato², Chiaki Sanbo¹, Shuji Shigenobu³, Yasuyuki Ohkawa⁴, Takeshi Fuchigami⁵, Yusuke Miyanari⁶

Affiliations

¹ Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan.
² Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS), Okazaki, 444-8787, Japan.
³ National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan.
⁴ Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan.
⁵ Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan.
⁶ Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan. Electronic address: [email protected].

PMID: 32353257
DOI: 10.1016/j.molcel.2020.04.004

Abstract

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

Substances

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