Basler, F. | Search bioRxiv

bioRxiv2026

Differences in substrate engagement and Retinoblastoma protein (RB) binding of human KDM5A and KDM5B

Trimethylation of lysine 4 of histone H3 (H3K4me3) is a post-translational modification (PTM) enriched at promoters of actively transcribed genes. H3K4me3 is removed by the human histone demethylases of the KDM5 family. KDM5 demethylases act as transcriptional repressors through their catalytic activity in addition to more complex roles that depend on their interactions with other chromatin regulators and may be independent of demethylase activity. To better understand the mechanistic differences of the closely related paralogs KDM5A and KDM5B as well as their interactions with Retinoblastoma protein (RB), we systematically analyzed and compared their demethylase activities, nucleosome engagement, and RB binding. We used recombinant nucleosome binding and demethylase activity assays, as well as an integrative structural biology approach using negative-stain electron microscopy (EM), AlphaFold predictions, and cross-linking mass spectrometry for a comprehensive in vitro analysis of these critical and largely non-redundant enzymes. KDM5A and KDM5B showed differences in enzyme kinetics using peptide substrates, as well as in nucleosome binding. Furthermore, KDM5A interacts with RB, mainly mediated by its canonical LxCxE RB binding motif. KDM5B, on the other hand, lacks an LxCxE binding motif and does not stably bind to RB under the conditions tested here. RB directly interacts with nucleosomes, and its nucleosome binding does not measurably affect KDM5A demethylase activity or nucleosome interactions. Our findings provide a biochemical framework for the differences between KDM5A and KDM5B regarding RB interactions and nucleosome engagement.

biochemistry↗

bioRxiv2025

Phosphoinositide- and Collybistin-Dependent Synaptic Clustering of Gephyrin

Gephyrin is the main scaffolding protein at inhibitory synapses clustering glycine and GABA type A receptors. At specific GABAergic synapses, the nucleotide exchange factor collybistin recruits gephyrin to the postsynaptic membrane via interaction with phosphoinositides. However, the molecular mechanisms underlying the formation, maintenance and regulation of collybistin-dependent gephyrin clusters remain poorly understood. This study sheds light on the molecular mechanism of gephyrin cluster formation based on gephyrin self-oligomerization induced by collybistin, leading to the formation of a high-molecular weight (>5 MDa) gephyrin-collybistin complex, which is regulated in two ways: First, plasma-membrane phosphoinositides promote complex formation demonstrating their critical role in membrane targeting and stabilization of gephyrin-collybistin clusters at postsynaptic sites. Second, gephyrin phosphorylation at Ser325 abolishes complex formation with collybistin thus impairing collybistin-dependent gephyrin clustering at GABAergic synapses. Collectively, our data demonstrates a molecular mechanism for synaptic clustering of gephyrin which involves collybistin- and phosphoinositide-dependent formation of high-molecular gephyrin oligomers.

biochemistry↗