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Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

ABSTRACT: Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

PROVIDER: PRJNA886978 | ENA |

REPOSITORIES: ENA

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Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development.

Project description:Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development.

| PRJNA886975 | ENA

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

Project description:Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

| PRJNA886977 | ENA

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]

Project description:Development of wheat (Triticum aestivum L.) grain mainly depends on the processes of starch synthesis and storage protein accumulation, which are critical for grain yield and quality. However, the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear. Here, we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes. We found that the chromatin accessibility changes are tightly associated with differential expressions and the proportion of distal ACRs were increased gradually during grain development. Specific transcription factor (TF) binding sites were enriched at different stages, and were diversified among the 3 subgenomes. We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles. Overall, our findings have provided numerous resources and illustrated the regulatory network during wheat grain development, which would shed lights on the improvement of wheat yields and qualities.

2023-02-15 | GSE214738 | GEO

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq]

2023-02-15 | GSE214737 | GEO

Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

Project description:Common wheat (T. aestivum) converged three subgenomes adapted to different environments. The combinatorial interaction between transcription factors (TFs) and regulatory elements (REs) defines a regulatory circuit that underlies subgenome convergence and divergence. Compared to the relatively conserved gene composition across subgenomes, the intergenic regions with abundant REs is drastically diversified by almost complete TE turnovers, raising major questions regarding how subgenome convergent and divergent regulation is encoded in the highly diversified intergenic regions, and the impact of TE evolution on regulatory conservation and innovation. In the present study, we created genome-wide TF binding catalog to assemble an extensive wheat regulatory network comprising connections among 182 TFs. The different effects of ancient and recent TE insertions on regulatory specificity were observed. Subgenome asymmetric TE expansion is an important source of subgenome divergent TFBS, which help explain the vast occupancy difference across subgenomes. Interestingly, the ancient expansion of RLC_famc1.4-derived TFBS occurred in more than 25% triads promoters. A significant fraction of these TE-derived TFBS subjected to region-specific evolutionary selections, resulting in subgenome-balanced TF binding but unbalanced degeneration of flanking TE sequences. These TE-derived subgenome convergent and divergent regulation linked to subgenome conserved and diversified pathways, suggesting that TEs are an important regulatory driving force contributed to polyploid evolution. Overall, this study demonstrated the impact of TEs on shaping the plasticity and adaptation of common wheat, enriched the theories of TE-promoted transcriptional innovation from the evolutionary aspects of polyploid regulation since first reported by McClintock.

2022-10-08 | GSE192815 | GEO

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-02-15 | GSE214739 | GEO

An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses

Project description:Wheat (Triticum aestivum) has a large allohexaploid genome. Subgenome-divergent regulation contributed to genome plasticity and the domestication of polyploid wheat. However, the specificity encoded in the wheat genome determining subgenome-divergent spatio-temporal regulation has been largely unexplored. The considerable size and complexity of the genome are major obstacles to dissecting the regulatory specificity. Here, we compared the epigenomes and transcriptomes from a large set of samples under diverse developmental and environmental conditions. Thousands of distal epigenetic regulatory elements (distal-epiREs) were specifically linked to their target promoters with coordinated epigenomic changes. We revealed that subgenome-divergent activity of homologous regulatory elements are affected by specific epigenetic signatures. Subgenome-divergent epiRE regulation of tissue specificity is associated with dynamic modulation of H3K27me3 mediated by Polycomb complex and demethylases. Furthermore, quantitative epigenomic approaches detected key stress responsive cis- and trans-acting factors validated by DNA Affinity Purification and sequencing (DAP-seq), and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Thus, this study provides a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat.

2021-02-04 | GSE139019 | GEO

Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development

Project description:Transcription start site (TSS) is the hub integrating regulatory input from promoters and enhancers. Common wheat converged three subgenomes adapted to different environment and established as a major crop worldwide. Detection of more precise and new TSS of both genes and enhancers in common wheat is the basis in interpreting transcriptional regulatory networks as well as the subgenome divergent regulation in their entirety.

2023-10-12 | GSE198284 | GEO

Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

Project description:Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

| PRJNA793259 | ENA

LHP1-mediated conditional repression of subgenome-diversified defenses is responsible for the high plasticity of allopolyploid wheat

Project description:High plasticity of common wheat is attributed to the captured and polyploidization-promoted diversity. However, uncontrolled subgenome diversification can lead to hybrid conflict and dysgenesis, resulting in decreased diversity. How genomic diversity is maintained and interpreted to increase plasticity is unclear. By data-mining from the binding of 193 genome-wide trans-factors and genetic perturbations in common wheat, we identified LHP1 as a major regulator of subgenome-diversified defense genes, enhancer RNAs, and metabolite synthesis-related gene clusters via H3K27me3. Stripe rust infection leads to a global decrease in LHP1-mediated H3K27me3, deprivation of which enhances common wheat stripe rust resistance. We also revealed the consistency between subgenome diversity and population diversity, potentially promoted by LHP1, implying the recent diversification preferentially occurred in the captured subgenome-diversified regions regulated by LHP1. Thus, common wheat benefitted from multi-faced role of LHP1 in promoting sequence diversity and repressing subgenome-diversified defenses; this constraint is eliminated by pathogen infections, enabling timely release and fixation of favorable variations, conferring the evolutionary advantage and high plasticity of common wheat.

2023-10-12 | GSE218538 | GEO

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