Introduction: Nucleosomes harboring specific histone variants show distinct chromatin localization patterns and regulatory functions, thereby playing crucial roles in epigenetic regulation. Compared to the well-understood variants of H2A and H3, the study about H2B variants is emerging. Deciphering the roles and regulatory mechanisms of H2B variants in plants will provide more knowledges about epigenetic regulations in plant biology.
Objectives: Using the model plant Arabidopsis thaliana as the research subject, we systematically analyzed histone H2B variants, four short N-terminal histone H2B variants (snH2Bs) were identified. The genomic distribution characteristics of these snH2Bs, their impact on plant growth, and the potential regulatory mechanisms were studied.
Methods: By integrating whole-genome chromatin immunoprecipitation sequencing (ChIP-seq) and fluorescence microscopy localization analysis, the distribution of snH2Bs across the genome was identified. Single, double, and triple knock-out mutants were constructed using CRISPR-Cas9 to further explore the functions of snH2Bs in the growth process of Arabidopsis thaliana, the possible mechanisms were also discussed.
Results: These snH2B variants are preferentially expressed in reproductive tissues and are detected in the nuclei of pollen grains. Further genome-wide profiling indicates that the snH2Bs distribute at active chromatin regions and are positively correlated with gene expression. By creating knock-out single, double, and triple mutants for these snH2Bs, we demonstrate that H2B.5 influences vegetative to reproductive transition. We also show that H2B.5 is required for proper accumulation of H3 lysine 9 acetylation and H2B mono-ubiquitination.
Conclusion: Overall, our study not only provide insights into the functions and chromatin characteristics of plant snH2Bs, but also supplies examples that illustrate the interplay between histone variants and histone modification. These findings contribute to the understanding of the fundamental principles of epigenetic regulation in eukaryotes and also highlight potential targets for crop improvement.
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http://dx.doi.org/10.1016/j.jare.2024.12.001 | DOI Listing |
Genes Genet Syst
December 2024
Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University.
Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from Archaean homologs; however, how this occurred remains unclear. Our previous genetic analysis on the budding yeast nucleosome identified 26 histone residues conserved between S.
View Article and Find Full Text PDFJ Adv Res
December 2024
Department of Urology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Hubei Hongshan Laboratory, Wuhan 430071, China. Electronic address:
bioRxiv
November 2024
Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
A cell's ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory.
View Article and Find Full Text PDFCommun Biol
November 2024
Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
As a fundamental unit for packaging genomic DNA into chromatin, the eukaryotic nucleosome core comprises a canonical octamer with two copies for each histone, H2A, H2B, H3, and H4, wrapped around with 147 base pairs of DNA. While H3 and H4 share structure-fold with archaeal histone-like proteins, the eukaryotic nucleosome core and the complete nucleosome (the core plus H1 histone) are unique to eukaryotes. To explore whether the eukaryotic nucleosome can assemble in prokaryotes and to reconstruct the possible route for its emergence in eukaryogenesis, we developed an in vivo system for assembly of nucleosomes in the model bacterium, Escherichia coli, and successfully reconstituted the core nucleosome, the complete nucleosome, and unexpectedly the non-canonical (H3-H4) octasome.
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