PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation

Abstract

DNA damage; Histone demethylation; Neural stem cells

Daño del ADN; Desmetilación de histonas; Células madre neurales

Dany a l'ADN; Desmetilació d'histones; Cèl·lules mare neuronals

Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me remains limited. To address this question, we used neural stem cells to analyze the function of the H3K9me2 demethylase PHF2, which is crucial for progenitor proliferation. Through mass-spectroscopy and genome-wide assays, we show that PHF2 interacts with heterochromatin components and is enriched at pericentromeric heterochromatin (PcH) boundaries where it maintains transcriptional activity. This binding is essential for silencing the satellite repeats, preventing DNA damage and genome instability. PHF2’s depletion increases the transcription of heterochromatic repeats, accompanied by a decrease in H3K9me3 levels and alterations in PcH organization. We further show that PHF2’s PHD and catalytic domains are crucial for maintaining PcH stability, thereby safeguarding genome integrity. These results highlight the multifaceted nature of PHF2’s functions in maintaining heterochromatin stability and regulating gene expression during neural development. Our study unravels the intricate relationship between heterochromatin stability and progenitor proliferation during mammalian neurogenesis.

We would like to thank Drs Jiemin Wong, and Jiwen Li for the PHF2 plasmid. Dr T Jenuwein for pCMV-FLAG-SUV39H1 plasmid. Dr B Garfinkel for pCDNA3.1-HPIBP3-HA plasmid. Drs I Amelio and A Jeltsch for p3xFlag-MaSat-NLS-ZF18-mVenusN and p3xFlag-mVenusC-HP1b-chromodomain plasmids. Drs J. Bernues, F. Azorín, A. Vaquero, C. Gallego, M. Arbonés, M. Beato, and S Sanchez-Molina for reagents and suggestions. All member of the team for helpful comments. This study was supported by grants BFU2015-69248-P, PGC2018-096082-B-I00 and PID2021-125862NB-I00 to MAMB from the Spanish Ministry of Economy to MAMB, FPI grant PRE2019-087498 to SAI.