Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE209645 | GEO | 2022/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209643 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition. Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant
2022-12-01 | GSE209642 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209641 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209638 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209640 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
2022-12-01 | GSE209644 | GEO
Project description:The H2A/UBIQUITIN-binding proteins AtZRF1a/b have been reported as key regulators involved in multiple processes of Arabidopsis plant growth and development. Yet, the cellular and molecular mechanisms underlying the mutant phenotype remain largely elusive. Here we show that loss-of-function of AtZRF1a/b causes defective root elongation and deformed root apical meristem organization in seedlings. The premature termination of the primary root in the atzrf1a;atzrf1b double mutant is associated with an advanced onset of endoreduplication and subsequent consumption of reservoir stem cells. Cytological analyses using cell type-specific markers and florescent dyes indicate that AtZRF1a/b are involved in maintenance of proper cell layer organization, determinacy of cell identity, and establishment of auxin gradient and maximum at the root tip. During embryogenesis AtZRF1a/b act dominantly in regulating the maintenance of ground tissue initial cells and production of lateral root cap. Lastly, quantitative real-time polymerase chain reaction analysis shows mis-expression of some key genes involved in regulating cell patterning, cell proliferation and/or hormone pathways. Our results provide important insight into AtZRF1a/b function in cell fate determinacy and in establishment and maintenance of proper stem cell reservoir during embryonic and post-embryonic root development.
| S-EPMC6882920 | biostudies-literature
Project description:BACKGROUND: Flowering plant development is wholly reliant on growth from meristems, which contain totipotent cells that give rise to all post-embryonic organs in the plant. Plants are uniquely able to alter their development throughout their lifespan through the generation of new organs in response to external signals. To identify genes that regulate meristem-based growth, we considered homologues of Raptor proteins, which regulate cell growth in response to nutrients in yeast and metazoans as part of a signaling complex with the target of rapamycin (TOR) kinase. RESULTS: We identified AtRaptor1A and AtRaptor1B, two loci predicted to encode Raptor proteins in Arabidopsis. Disruption of AtRaptor1B yields plants with a wide range of developmental defects: roots are thick and grow slowly, leaf initiation and bolting are delayed and the shoot inflorescence shows reduced apical dominance. AtRaptor1A AtRaptor1B double mutants show normal embryonic development but are unable to maintain post-embryonic meristem-driven growth. AtRaptor transcripts accumulate in dividing and expanding cells and tissues. CONCLUSION: The data implicate the TOR signaling pathway, a major regulator of cell growth in yeast and metazoans, in the maintenance of growth from the shoot apical meristem in plants. These results provide insights into the ways in which TOR/Raptor signaling has been adapted to regulate plant growth and development, and indicate that in plants, as in other eukaryotes, there is some Raptor-independent TOR activity.
| S-EPMC1131892 | biostudies-literature
Project description:BACKGROUND: Histone variants establish structural and functional diversity of chromatin by affecting nucleosome stability and histone-protein interactions. H3.3 is an H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. In animals, H3.3 is associated with active transcription and possibly maintenance of transcriptional memory. Plant H3 variants, which evolved independently of their animal counterparts, are much less well understood. RESULTS: We profile the H3.3 distribution in Arabidopsis at mono-nucleosomal resolution using native chromatin immunoprecipitation. This results in the precise mapping of H3.3-containing nucleosomes, which are not only enriched in gene bodies as previously reported, but also at a subset of promoter regions and downstream of the 3' ends of active genes. While H3.3 presence within transcribed regions is strongly associated with transcriptional activity, H3.3 at promoters is often independent of transcription. In particular, promoters with GA motifs carry H3.3 regardless of the gene expression levels. H3.3 on promoters of inactive genes is associated with H3K27me3 at gene bodies. In addition, H3.3-enriched plant promoters often contain RNA Pol II considerably upstream of the transcriptional start site. H3.3 and RNA Pol II are found on active as well as on inactive promoters and are enriched at strongly regulated genes. CONCLUSIONS: In animals and plants, H3.3 organizes chromatin in transcribed regions and in promoters. The results suggest a function of H3.3 in transcriptional regulation and support a model that a single ancestral H3 evolved into H3 variants with similar sub-functionalization patterns in plants and animals.
| S-EPMC4054674 | biostudies-literature
Project description:Mature oocyte cytoplasm can reprogram somatic cell nuclei to the pluripotent state through a series of sequential events including protein exchange between the donor nucleus and ooplasm, chromatin remodeling, and pluripotency gene reactivation. Maternal factors that are responsible for this reprogramming process remain largely unidentified. Here, we demonstrate that knockdown of histone variant H3.3 in mouse oocytes results in compromised reprogramming and down-regulation of key pluripotency genes; and this compromised reprogramming for developmental potentials and transcription of pluripotency genes can be rescued by injecting exogenous H3.3 mRNA, but not H3.2 mRNA, into oocytes in somatic cell nuclear transfer embryos. We show that maternal H3.3, and not H3.3 in the donor nucleus, is essential for successful reprogramming of somatic cell nucleus into the pluripotent state. Furthermore, H3.3 is involved in this reprogramming process by remodeling the donor nuclear chromatin through replacement of donor nucleus-derived H3 with de novo synthesized maternal H3.3 protein. Our study shows that H3.3 is a crucial maternal factor for oocyte reprogramming and provides a practical model to directly dissect the oocyte for its reprogramming capacity.
| S-EPMC4034224 | biostudies-literature