Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

Abstract

Background Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. Results Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. Conclusions Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.

Epigenetic modifications mediate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat

“…The majority of histone modification peaks were located in the distal region expected for H3K36me3 in wheat (Fig. S1d), as described in our recent report (Zhao et al, 2023). H3K27ac and H3K4me3 were associated with highly expressed genes, while H3K27me3 is enriched in low/non-expressed genes (Fig.…”

“…CUT&Tag experiment were done follow the previous described method (Zhao et al, 2023). The nuclei were extracted by chooping fresh samples soaked in the HBM buffer (25 mM Tris-HCl pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM Beta-mercaptoethanol, 2 mM spermine, 1 mM PMSF, EDTA-free protease inhibitor cocktail).…”

Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat

“…The majority of histone modification peaks were located in the distal region expected for H3K36me3 in wheat (Fig. S1c), as described in our recent report 19 . H3K27ac and H3K4me3 were associated with highly expressed genes, while H3K27me3 is enriched in low/non-expressed genes (Fig.…”

“…Total RNA was extracted using HiPure Plant RNA Mini Kit according to the manufacturer's instructions (Magen, R4111-02), and libraries were sequenced using an Illumina Novaseq platform. CUT&Tag experiment were done follow the previous described method 19 . The nuclei were extracted by chooping fresh samples soaked in the HBM buffer (25 mM Tris-HCl pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM Beta-mercaptoethanol, 2 mM spermine, 1 mM PMSF, EDTA-free protease inhibitor cocktail).…”

“…In this study, we used the CUT&Tag 18,19 to profile epigenomic modifications in two wheat cultivars, KN9204 and J411, for various histone modifications and histone variant in three different tissues under varying nitrogen conditions. Our epigenomic maps offer a comprehensive understanding of the dynamic chromatin landscapes of these two wheat cultivars in response to low nitrogen conditions.…”