In most organisms, excluding archaea and a few eubacteria, histones–the proteins around which DNA is tightly wound in a chromosome– keep the DNA neatly organised and packed in the cell.
Histone proteins—H2A, H2B, H3, and H4—and their modified forms or variants assemble into an octamer to form the nucleosome. Chemical modifications to these histones, such as the addition or removal of specific amino acid residues, influence how tightly or loosely the DNA is wound around the nucleosome. This governs access to DNA and plays a crucial role in regulating gene expression, DNA modifications, chromosomal architecture, and the activation or silencing of genes. While a variety of histone variants, particularly those of H2A, H2B, and H3, have been identified in both plants and animals, with roles in processes such as chromosome segregation and DNA repair, very few variants of H4 have been reported, and those identified are primarily found in parasitic organisms.
In a first, Dr P.V. Shivaprasad’s group at NCBS has identified a new H4 histone variant in rice that enhances the plant's tolerance to salt stress.
“We were looking for different histone-coding genes across all plants. When we found this variant in rice, it immediately caught our attention because H4 is typically highly conserved, and its variants are extremely rare. This particular variant appeared consistently across all rice families, but not in other plants. That unexpected pattern was the starting point for our study,” says Vivek Hari-Sunder Gandhivel, lead author of the study. Plants have varied response mechanisms to deal with biotic and abiotic stress, much of which is controlled by changes in their genetic make-up through modifications of histones. While most studies on the role of histones and their variants in stress response are conducted in the model plant Arabidopsis, which has small and compartmentalised chromatin, the regulation of chromatin in complex species with large genomes, such as rice, remains unclear.
Histone Regulation and Stress Responses
This study used molecular, genetic, and genomic methods to explore the role of the H4 variant in genome regulation. It suggests that this variant may have helped semi-aquatic rice varieties adapt to changing environments.
To confirm that H4.V was not only present in the genome but also functional, the team used microscopy and chromatin immunoprecipitation sequencing. They found that H4.V is not only expressed but is actively incorporated into nucleosomes at specific locations along the genome. To probe its function, the researchers used CRISPR-based gene editing to knock out H4.V in rice plants. They found that these mutant plants were stunted, had small seeds, and showed poor reproductive growth. That alone confirmed H4.V plays a vital role in development.
But a deeper dive into the plants’ transcriptome– a profile of all the genes being expressed– revealed something even more intriguing. “In wild-type plants, genes related to salt stress are only turned on when needed. But in the mutants, those same genes were being expressed all the time”, said Vivek. “It’s like the plant thought it was under constant attack”.
Histones don’t just passively hold DNA. Their chemical modifications, such as acetylation, can activate or silence genes. H4 is known to be acetylated at specific sites to allow stress-response genes to turn on when needed. When H4.V is incorporated into a nucleosome, it replaces canonical H4, displacing the acetylation marks as well, actively rewiring which genes are turned on or off, depending on where it's incorporated. To understand this at a molecular level, the team solved the atomic-resolution structure of the rice nucleosome. The structural data revealed that a single amino acid change (alanine to valine at position 33) altered how H4.V interacts with DNA and other histones, potentially affecting nucleosome stability and how densely packed chromatin will be.
The team also suggests that H4.V helps modulate a wide network of stress-response genes, including those related to jasmonic acid signalling, a key hormone pathway for salt and drought stress. They found that several sodium ion transporters were also misregulated in the mutants, which would explain their poor survival and growth.
The team believes H4.V works as a molecular switch that enables plants to toggle between growth and stress response. In normal conditions, the plant invests energy in growth. Under salt stress, H4.V repositions itself across the genome to activate the genes needed to survive harsh environments.
Toward Climate-Resilient Crops
Rice is often grown in semi-aquatic or coastal regions, where rising salinity due to climate change threatens crop productivity. Understanding the molecular basis of its ability to cope with environmental stressors in its natural ecosystem is essential to utilise these mechanisms to incorporate them in high-yielding cultivated rice lines.
“Histone variants are the major upstream players in epigenetic changes, and the newly identified player offers a new tool to understand the basis of epigenetic changes in rice. The identification of H4.V opens up new possibilities for engineering or breeding salt-tolerant rice varieties—not by modifying dozens of stress-related genes individually, but by tweaking a single regulatory hub”, said Dr Shivaprasad, senior author of the study.
0 Comments