Casas-Mollano, J. A. | Search bioRxiv

bioRxiv2025

Mass Spectrometry-Based Characterization of Histone Post-Translational Modifications in Sugarcane

Histones, the core components of nucleosomes, play an important role in chromatin structure and function through post-translational modifications (PTMs) that regulate gene expression without altering the DNA sequence. Sugarcane (Saccharum spp.), a highly polyploid and economically significant crop, has a complex genome with a limited understanding of histone PTMs. In this study, we employed mass spectrometry to characterise the PTMs of histones in internodes of field-grown commercial sugarcane, harvested at different times of the day, with a focus on histones H2A and H2B, which had not been previously studied in this context. Using a sorghum histone catalog as a reference, we identified 26 H1, 91 H2A, 70 H2B, 5 CENH3, 36 H3.1, 23 H3.3, 18 H3.3L, and 57 H4 loci in the sugarcane genome. We detected extensive PTMs, including acetylation and methylation, across histones H2A, H2B, H3, and H4. Canonical and variant histones showed distinct post-translational modification (PTM) patterns, highlighting their functional specialisation. This study provides a comprehensive catalog of sugarcane histone PTMs, offering insights into their roles in chromatin dynamics and gene regulation, with potential applications in crop improvement and stress adaptation.

plant biology↗

bioRxiv2022

Optimized dCas9 Transcription Activators for Plants

Understanding how gene expression impacts plant development and physiology is important for rationally engineering improved crops. Programmable Transcriptional Activators (PTAs), including CRISPR-Cas activators, have traditionally relied on a limited number of transcriptional activation domains. Usually the VP64 domain, derived from human herpes simplex virus, is fused to a DNA-binding domain to activate target gene expression. We reasoned there was considerable space for PTA improvement by replacing VP64 with a plant-derived activation domain. To address this, we designed, built, and tested a PTA library of 38 putative plant transcriptional activation domains. Domains from HSFA6b, AvrXa10, DOF1, DREB1, and DREB2 genes function as strong activators in Setaria viridis and Arabidopsis thaliana in protoplast assays and in transgenic plants. Overexpression of multiple endogenous genes (FT, PAP1, WUS) reached levels similar to the highly expressed housekeeping gene, PP2A, regardless of basal expression level. Further, these domains were effective in different PTA architectures, including the dCas9-SunTag, dCas9-Moontag, and TALE-SunTag systems. Lastly, we demonstrate the ability of these improved PTAs to map enhancer regions that promote gene expression in plants. This work demonstrates the effective and flexible nature of PTAs to activate target genes in plants, providing tools that can be used to improve agronomically relevant traits of interest.

plant biology↗