Neuronal splicing of the unmethylated histone H3K4 reader, PHF21A, prevents excessive synaptogenesis

Masayoshi Nagai; Robert S Porter; Maxwell Miyasato; Aijia Wang; Cecilia M Gavilan; Elizabeth D Hughes; Michael C Wu; Thomas L Saunders; Shigeki Iwase

doi:10.1016/j.jbc.2024.107881

Neuronal splicing of the unmethylated histone H3K4 reader, PHF21A, prevents excessive synaptogenesis

J Biol Chem. 2024 Oct 10:107881. doi: 10.1016/j.jbc.2024.107881. Online ahead of print.

Authors

Masayoshi Nagai¹, Robert S Porter², Maxwell Miyasato³, Aijia Wang⁴, Cecilia M Gavilan², Elizabeth D Hughes⁵, Michael C Wu⁶, Thomas L Saunders⁷, Shigeki Iwase⁸

Affiliations

¹ Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
² Genetics & Genomics Graduate Program, University of Michigan, MI, 48109, USA.
³ Neuroscience Graduate Program, University of Michigan, MI, 48109, USA.
⁴ University of Michigan College of Literature, Science, and the Arts, MI, 48109, USA.
⁵ Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA.
⁶ Neurodigitech, LLC, San Diego, CA 92126, USA.
⁷ Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA; Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School.
⁸ Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: siwase@umich.edu.

PMID: 39395799
DOI: 10.1016/j.jbc.2024.107881

Abstract

PHF21A is a histone-binding protein that recognizes unmethylated histone H3K4, the reaction product of LSD1 histone demethylase. PHF21A and LSD1 form a complex, and both undergo neuron-specific microexon splicing. The PHF21A neuronal microexon interferes with nucleosome binding, whereas the LSD1 neuronal microexon weakens H3K4 demethylation activity and can alter the substrate specificity to H3K9 or H4K20. However, the temporal expression patterns of PHF21A and LSD1 splicing isoforms during brain development and their biological roles remain unknown. In this work, we report that neuronal PHF21A isoform expression precedes neuronal LSD1 expression during human neuron differentiation and mouse brain development. The asynchronous splicing events resulted in stepwise deactivation of the LSD1-PHF21A complex in reversing H3K4 methylation. An unbiased proteomics survey revealed that the enzymatically inactive LSD1-PHF21A complex interacts with neuron-specific binding partners, including MYT1-family transcription factors and post-transcriptional mRNA processing proteins such as VIRMA. The interaction with the neuron-specific components, however, did not require the PHF21A microexon, indicating that the neuronal proteomic milieu, rather than the microexon-encoded PHF21A segment, is responsible for neuron-specific complex formation. Finally, by using two Phf21a mutant mouse models, we found that Phf21a neuronal splicing prevents excess synapse formation that otherwise would occur when canonical PHF21A is expressed in neurons. These results suggest that the role of the PHF21A microexon is to dampen LSD1-mediated H3K4 demethylation, thereby containing aberrant synaptogenesis.

Keywords: LSD1; PHF21A; histone demethylase; histone methylation; microexon splicing.