Biology subjects

Binenbaum, J.

Publications and source records attributed to Binenbaum, J..

3 recordsLinked to original sources

bioRxiv2026

Engineering chromatin to encode transcriptional immune memory in Arabidopsis

Transcriptional memory enables organisms to respond more rapidly to recurrent stress, yet the underlying features of chromatin that contribute to this transcriptional recalibration remain poorly defined. Here we identify the genes displaying transcriptional memory in response to the bacterial immune elicitor, flg22, in Arabidopsis thaliana. In comparison to non-memory response genes, these memory genes show a preference for tissue-specific over uniform spatial expression patterning. The chromatin architecture of these genes in the resting state displays depletion of H3K4me3, elevation H3K27me3 and a subset are marked by H3K27me3-H3K4me3 bivalency. The H3K4me3 demethylase, JMJ14, is required for transcriptional memory, with JMJ14 occupancy enriched over memory gene loci. Upon priming, chromatin is reconfigured, with H3K4me3 levels increasing in a sustained manner at memory gene loci. To assess the function of this H3K4me3 accrual, we employ epigenome-engineering, observing that its targeted deposition at memory gene loci, including the WRKY29 locus, is sufficient to drive transcriptional memory and can endow plants with enhanced resistance to the bacterial pathogen, Pseudomonas syringae. Together, the findings demonstrate a causal role for H3K4me3 in transcriptional memory, under the regulation of JMJ14, and open the door for rational rewriting of chromatin to enhance organismal resilience.

plant biology↗

bioRxiv2025

Triphenylphosphonium is an effective targeting moiety for plants mitochondria

Small signaling molecule regulates key physiological processes in plants, often in a spatially distinct manner. However, current methods for applying small-molecules, endogenous or synthetic, in plants research lack spatial precision, limiting the ability to study and utilize their localized effects. Here, we validate triphenylphosphonium (TPP) as a mitochondrial targeting motif in plants. Using fluorescently labeled TPP conjugates in Arabidopsis thaliana, we demonstrate mitochondria-specific accumulation, even in the presence of plastids. This precise localization enables detailed imaging of mitochondria and mitochondrial DNA in living plants. We further exploit this targeting ability by developing a TPP-ciprofloxacin conjugate to selectively inhibit mitochondrial DNA gyrase, an enzyme involved in organellar DNA replication. Unlike free ciprofloxacin, which disrupts both mitochondrial and chloroplast DNA gyrase activity, the TPP-conjugate specifically targets mitochondrial gyrase, leading to slower plant growth without affecting chloroplast function. This targeted inhibition triggers a mitochondrial retrograde response, characterized by increased reactive oxygen species levels and the upregulation of stress-response genes in the nucleus. Our findings establish TPP as a reliable tool for mitochondrial targeting in plants and open avenues for both fundamental research and agricultural applications. By enabling organelle-specific manipulation in species not amenable to genetic engineering, TPP-based strategies have potential for advancing plant biology and precision agriculture.

plant biology↗

bioRxiv2025

CRISPR targeting of H3K4me3 activates gene expression and unlocks centromeric crossover recombination in Arabidopsis

H3K4me3 is a fundamental and highly conserved chromatin mark across eukaryotes, playing a central role in many genome-related processes, including transcription, maintenance of cell identity, DNA damage repair, and meiotic recombination. However, identifying the causal function of H3K4me3 in these diverse pathways remains a challenge, and we lack the tools to manipulate it for agricultural benefit. Here we use the CRISPR-based SunTag system to direct H3K4me3 methyltransferases in the model plant, Arabidopsis thaliana. Targeting of SunTag-SDG2 activates the expression of the endogenous reporter gene, FWA. We show that SunTag-SDG2 can be employed to increase pathogen resistance by targeting the H3K4me3-dependent disease resistance gene, SNC1. Meiotic crossover recombination rates impose a limit on the speed with which new traits can be transferred to elite crop varieties. We demonstrate that targeting of SunTag-SDG2 to low recombining centromeric regions can significantly stimulate proximal crossover formation. Finally, we reveal that the effect is not specific to SDG2 and is likely dependent on the H3K4me3 mark itself, as the orthogonal mammalian-derived H3K4me3 methyltransferase, PRDM9, produces a similar effect on gene expression with reduced off-target potential. Overall, our study supports an instructive role for H3K4me3 in transcription and meiotic recombination and opens the door to precise modulation of important agricultural traits.

plant biology↗