Biology subjects

Joseph, F. M.

Publications and source records attributed to Joseph, F. M..

3 recordsLinked to original sources

bioRxiv2026

H2AX C-Terminal Dipeptide Truncation: A Master Switch of the DNA Damage Response.

Phosphorylation of histone H2AX at serine 139 ({gamma}H2AX) by ATM/ATR kinases is a central marker of the DNA damage response (DDR), widely used to detect DNA double-strand breaks. However, the molecular basis for tissue- and context-specific variation in {gamma}H2AX signaling remains poorly defined. Here we discover a post-translational truncation of H2AX, catalyzed by lysine demethylase 4A (KDM4A), which removes two C-terminal amino acids critical for ATM/ATR-dependent phosphorylation. This truncation renders H2AX refractory to {gamma}H2AX formation, effectively bypassing canonical DDR signaling. Truncated H2AX accumulates in select cell lines, primary cells, solid tumors, and normal tissues. Genetic knockdown or pharmacologic inhibition of KDM4A reduces H2AX truncation, restores {gamma}H2AX induction, and enhances DNA repair capacity. Conversely, KDM4A overexpression promotes H2AX truncation, impairs {gamma}H2AX signaling, and exacerbates DNA damage accumulation. This previously unrecognized regulatory axis implicates KDM4A catalyzed H2AX truncation as a superseding mechanism that represses the canonical DDR and disrupts the correlation between {gamma}H2AX and DNA damage. This dioxygenase-based protease mechanism represents a new class of proteases and is the first example of c-terminal dipeptide protein truncation. This discovery has broad implications in the basic science of genome maintenance, wound healing, cancer, combinatorial therapy, precision medicine, and technologies such as gene editing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/723272v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1b4050forg.highwire.dtl.DTLVardef@1b8333aorg.highwire.dtl.DTLVardef@2b27c5org.highwire.dtl.DTLVardef@13ff699_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Regulation of ATAD2B bromodomain binding activity by the histone code

The ATPase family AAA+ domain containing 2 (ATAD2) protein, and its paralog ATAD2B, have a C-terminal bromodomain that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2 and ATAD2B bromodomains to select acetylated lysine among multiple histone post-translational modifications. Isothermal titration calorimetry experiments revealed that the ATAD2 and ATAD2B bromodomains selectively recognize distinct patterns of acetylated lysine residues on the N-terminal tails of histone proteins. Adjacent methylation or phosphorylation marks were found to either enhance or weaken the recognition of acetylated lysine by the ATAD2/B bromodomains. Complementary structural studies provide mechanistic insights into how residues within the bromodomain binding pocket coordinate the acetyllysine group in the context of adjacent post- translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands, either as onco mutations or as histone variants, impact the recognition of an adjacent acetylated lysine residue. In summary, our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2 and ATAD2B bromodomains, resulting in distinct binding modes of the two bromodomains. KEY POINTSO_LIMultiple independent ATAD2 gene duplication events are evident during metazoan evolution, indicating expansion of functionality in the ATAD2 gene family and suggesting distinct functions for ATAD2 and ATAD2B. C_LIO_LIHigh-resolution structures of the ATAD2 and ATAD2B bromodomains in complex with their histone ligands demonstrate how multiple post-translational modifications are coordinated. C_LIO_LIRecognition of different subsets acetylated histone ligands by the ATAD2 and ATAD2B bromodomains is driven by unique features within the binding pockets of these paralogous proteins. C_LIO_LIOnco-histone mutations and histone variants that change the amino acid sequence of the histone tails modulate the ATAD2 and ATAD2B bromodomain activity. C_LIO_LIThis study demonstrates how the combinatorial activity of multiple post- translational modifications forms a histone code and influences the recognition of acetylated lysine by bromodomain-containing proteins. C_LI

biochemistry↗

bioRxiv2022

An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability

In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g., K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has broader extension. Here we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation chromatin switch on the H3 tail that modulates read-write accessibility in nucleosomes and resolve the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.

biochemistry↗