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Understanding Chromatin Modifiers in Plant Gene Expression
Chromatin, consisting of DNA and proteins, is fundamental in the nucleus of eukaryotic cells. Crucial in this complex are chromatin modifiers—proteins that chemically alter chromatin's structure. These modifiers significantly influence gene expression by adding or removing chemical groups to histones within the chromatin or directly to the DNA.
Recent Discoveries in Rice Genome
The recent study by Prof. Xianjun Song and his team from the Institute of Botany of the Chinese Academy of Sciences has brought to light new facets of this process in rice plants. Focusing on a ternary protein complex in rice nuclei that impacts grain size, the team observed that the transcription factor bZIP23 recruits the histone acetyltransferase HHC4 to specific DNA promoters. This discovery, detailed in Developmental Cell, advances our understanding of epigenetic regulation in crop development.
In prior research, Song highlighted the role of GRAIN WEIGHT 6a (GW6a), which encodes the histone acetyltransferase OsglHAT1, a positive regulator of grain size and yield. Dr. Shen Shaoyan, the study's first author, explained, “At the beginning of this study, we identified five rice homologs of OsglHAT1 on chromosomes 2, 3, 4, and 7 (hence named HHCs) and sought to investigate whether these homologs also modulate grain size. Interestingly, HHC4 regulates grain size but adopts a different cytological mechanism from GW6a."
Investigative Techniques and Findings
Employing molecular biology techniques like chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and immunoprecipitation followed by mass spectrometry (IP-MS), the team demonstrated direct interactions between bZIP23 and HHC4. The role of the bZIP23 gene in salinity, drought resistance, and seed vigor was already characterized, but its influence on grain size was a new revelation. Overexpression of bZIP23 not only enhanced grain size but also synergistically activated the expression of grain size regulators when co-targeted with HHC4.
Further analysis uncovered an interaction network involving HHC4, ADA2, and bZIP23, which enhances bZIP23 transactivation on target genes. Yeast two-hybrid (Y2H) screening revealed the GSK3-like kinase protein TGW3 also interacts with HHC4. Mutation analysis identified serine residues S189 and S190 of HHC4 as key phosphorylation sites by TGW3. This phosphorylation was shown to negatively affect several aspects of the HHC4 protein, including its stability and interaction with bZIP23.
Implications for Crop Yields
Field trials demonstrated the practical implications of these findings: HHC4 overexpression and TGW3 knockout led to an up to 24% increase in rice grain yield. These findings reveal a chromatin modifier-centered pathway as a crucial regulator of grain size in rice, offering promising avenues for high-yield crop breeding programs. However, as with all scientific endeavors, these results form a part of an ongoing journey to fully comprehend and harness the complexities of genetic regulation in crops.
Original Publication:
Shen S, Ma M, Bai C, et al. Optimizing rice grain size by attenuating phosphorylation-triggered functional impairment of a chromatin modifier ternary complex. Developmental Cell. Published online 2024. doi:https://doi.org/10.1016/j.devcel.2023.12.013