Biology subjects

Petronikolou, N.

Publications and source records attributed to Petronikolou, N..

3 recordsLinked to original sources

bioRxiv2025

An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA

Lysine demethylase 5A (KDM5A) plays a key role in the regulation of chromatin accessibility by catalyzing the removal of trimethyl marks on histone H3K4 (H3K4me3). KDM5A is also an oncogenic driver, with overexpression of KDM5A observed in various cancers, including breast, lung, and ovarian cancer. Past studies have characterized the functions of KDM5A domains, including KDM5A interactions with the histone H3 tail, but have yet to identify the broader mechanisms that drive KDM5A binding to the nucleosome. Through investigation of binding and catalysis on nucleosome substrates, we uncovered multivalent interactions of KDM5A with the H2A/H2B acidic patch and DNA that play crucial roles in the regulation of catalytic activity. We also identified an intrinsically disordered region (IDR) containing bifunctional arginine-rich motifs capable of binding to both the histone H2A/H2B acidic patch and nucleosomal DNA that is necessary for catalysis on nucleosome substrates. Our findings both elucidate previously unknown mechanisms that regulate KDM5A catalytic activity and reveal the ability of an IDR to engage in multiple interactions with chromatin. ARTICLE HIGHLIGHTSO_LIThe intrinsically disordered region of KDM5A binds the acidic patch and DNA. C_LIO_LIInteractions with the nucleosome are mediated by arginine-rich motifs in the IDR. C_LIO_LIThe IDR properly orients KDM5A on the nucleosome to enable catalysis. C_LI

biochemistry↗

bioRxiv2024

Monitoring lysosomal catabolism: a sensitive probe for assessing targeted lysosomal degradation of extracellular proteins

Extracellular targeted protein degradation (eTPD) is an emerging therapeutic field. The Lysosome targeting chimera (LYTAC) is a therapeutic modality that promotes degradation of extracellular drivers of disease in the lysosome. While widely available pH-sensitive probes may report on lysosome delivery, these probes do not necessarily report on the enzymatically active functional state of the lysosome. We report the development and application of a sensitive fluorescent probe, LysoLight Deep Red, to monitor catabolism of internalized proteins in the lysosome based on cleavage by cathepsin proteases. We demonstrate the application of Lysolight Deep Red to monitor the catabolic fate of therapeutic monoclonal antibodies, ASGPR-targeted LYTAC therapeutics and LYTAC targets in immortalized cell lines and in primary human hepatocytes.

cell biology↗

bioRxiv2019

Extended Recognition of the Histone H3 Tail by Histone Demethylase KDM5A

Human lysine demethylase KDM5A is a chromatin modifying enzyme associated with transcriptional regulation due to its ability to catalyze removal of methyl groups from methylated lysine 4 of histone H3 (H3K4me3). Amplification of KDM5A is observed in a number of cancers, including breast cancer, prostate cancer, hepatocellular carcinoma, lung cancer and gastric cancer. In this study, we employed alanine scanning mutagenesis to investigate substrate recognition of KDM5A and identify the H3 tail residues necessary for KDM5A-catalyzed demethylation. Our data show that the H3Q5 residue is critical for substrate recognition by KDM5A. Our data also reveal that the protein-protein interactions between KDM5A and the histone H3 tail extend beyond the amino acids proximal to the substrate mark. Specifically, demethylation activity assays show that deletion or mutation of residues at positions 14-18 on the H3 tail results in an 8-fold increase in the KMapp compared to wild-type 18mer peptide, suggesting this distal epitope is important in histone engagement. Finally, we demonstrate that post-translational modifications on this distal epitope can modulate KDM5A-dependent demethylation. Our findings provide insights into H3K4-specific recognition by KDM5A as well as how chromatin context can regulate KDM5A activity and H3K4 methylation status.

biochemistry↗