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Editing histones to explore epigenetic regulation of plant development

Histone proteins play a crucial role in the regulation of gene expression in eukaryotes. In a study published in the journal New Phytologist, scientists at IRIG have used a novel approach in plants to decipher the true functional impact of histones, revealing the key role of a modification carried by histone H3, in cell fate and metabolic regulation of stem lignin composition.

Published on 20 February 2023

​Eukaryotic DNA, by associating with histones, is organized into a structure named chromatin. On this chromatin, the so-called epigenetic marks allow precise and dynamic control of gene expression, which is necessary for the proper deployment of developmental programs. Among these marks, the post-translational modifications carried by histones have thus far been studied using mutants for the enzymes that catalyze them. This strategy has led to significant advances in the field of epigenetics. However, the multiple and redundant functions of the studied enzymes have prevented depicting the precise role of histone residues and the marks they carry.

Scientists at IRIG [collaboration] have sought to decipher the true function of Lysine 27 on histone H3 (H3K27) in more detail by developing a novel approach, published in New Phytologist.
This approach consists of having the model plant Arabidopsis thaliana express a histone H3 variant carrying an alanine instead of a lysine at position 27, inducing a drastic decrease in the level of methylation on H3K27. A detailed phenotypic analysis revealed strong developmental effects in the corresponding lines, some reminiscent of observations already made in enzymatic mutants, others singular and never demonstrated before. In addition to early flowering, curled leaves and accelerated proliferation of "callus" from undifferentiated cells, the lines obtained show shortened stems with altered organization into cell types. Transcriptomic and metabolomic analyses indicate that the latter phenotype is the result of a deregulation of metabolic fluxes in the phenylpropanoid and lignin biosynthetic pathway.

With this work, the scientists shed new light on the different roles played by lysine 27 of histone H3 in plants, including the regulation of key metabolic pathways involved in lignin composition and the control of stem elongation. This approach, applied to other histone protein residues or in other plant species, shall reveal new functions in the regulation of gene expression in development and response to environmental signals.

Figure: Arabidopsis plants expressing a modified form of histone H3 (K27A substitution of lysine 27 to alanine) show several morphological differences from control plants expressing an unmodified histone H3 (WT): early flowering and short stem, better callus proliferation, cell type defects on the epidermis and in the lower layers of the stem. Credit CEA​

Collaboration: the Institute of Plant Molecular Biology (IBMP) - CNRS in Strasbourg, and the Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - University of Jerusalem.

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