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Replication-independent eviction of H2B.8 reveals large-scale chromatin reprogramming during seed imbibition [ChIP_H2B8]

ABSTRACT: The transition from the seed to the seedling is a crucial developmental switch associated with changes in nuclear organization and extensive alterations in gene expression patterns. The extent to which this developmental transition involves chromatin dynamics and changes in the composition of the nucleosome in histone variants remains largely unexplored. Here we report that in Arabidopsis thaliana, the chromatin of dry seed embryos is characterized by the presence of the H2B.8 histone variant, which accumulates in a FACT-dependent manner, and forms heterotypic nucleosomes with other H2B variants at genes and transposons on chromosome arms. 3D microscopy and Hi-C analysis report that H2B.8 contributes to chromatin organization, with H2B.8-enriched chromatin regions forming clusters structuring the 3D nuclear space. H2B.8-marked genes are co-enriched with gene body H2A.Z and H3K27me3 and are transcriptionally repressed during the early stages of germination. During seed imbibition, we find that H2B.8 transcripts are degraded and H2B.8 histone variants evicted. This process operates independently of DNA replication but requires protein translation and de novo transcription. Histone eviction is not restricted to H2B.8 but also involves turnover of the histone variant H3.3. Imbibition therefore initiates a broad, replication-independent chromatin reprogramming process, highlighting a fundamental mechanism of epigenetic regulation during early plant development.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE304459 | GEO | 2026/05/12

REPOSITORIES: GEO

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Replication-independent eviction of H2B.8 reveals large-scale chromatin reprogramming during seed imbibition [RNAseq_24H]

Project description:The transition from the seed to the seedling is a crucial developmental switch associated with changes in nuclear organization and extensive alterations in gene expression patterns. The extent to which this developmental transition involves chromatin dynamics and changes in the composition of the nucleosome in histone variants remains largely unexplored. Here we report that in Arabidopsis thaliana, the chromatin of dry seed embryos is characterized by the presence of the H2B.8 histone variant, which accumulates in a FACT-dependent manner, and forms heterotypic nucleosomes with other H2B variants at genes and transposons on chromosome arms. 3D microscopy and Hi-C analysis report that H2B.8 contributes to chromatin organization, with H2B.8-enriched chromatin regions forming clusters structuring the 3D nuclear space. H2B.8-marked genes are co-enriched with gene body H2A.Z and H3K27me3 and are transcriptionally repressed during the early stages of germination. During seed imbibition, we find that H2B.8 transcripts are degraded and H2B.8 histone variants evicted. This process operates independently of DNA replication but requires protein translation and de novo transcription. Histone eviction is not restricted to H2B.8 but also involves turnover of the histone variant H3.3. Imbibition therefore initiates a broad, replication-independent chromatin reprogramming process, highlighting a fundamental mechanism of epigenetic regulation during early plant development.

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