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Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq]

ABSTRACT: Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq]

PROVIDER: PRJNA779997 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16932138_1.fastq.gz	Fastqsanger.gz
	SRR16932138_2.fastq.gz	Fastqsanger.gz
	SRR16932139_1.fastq.gz	Fastqsanger.gz
	SRR16932139_2.fastq.gz	Fastqsanger.gz
	SRR16932140_1.fastq.gz	Fastqsanger.gz

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Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [DAP-seq]

Project description:Expression divergence caused by genetic variation and crosstalks among subgenomes of the allohexaploid bread wheat (Triticum aestivum. L., BBAADD) is hypothesized to increase its adaptability and/or plasticity. However, the molecular basis of expression divergence remains unclear. Squamosa promoter-binding protein-like (SPL) transcription factors are critical for a wide array of biological processes. In this study, we constructed expression regulatory networks by combining DAP-seq for 40 SPLs, ATAC-seq, and RNA-seq. Our findings indicate that a group of low-affinity SPL binding regions (SBRs) were targeted by diverse SPLs and caused different sequence preferences around the core GTAC motif. The SBRs including the low-affinity ones are evolutionarily conserved, enriched GWAS signals related to important agricultural traits. However, those SBRs are highly diversified among the cis-regulatory regions (CREs) of syntenic genes, with less than 8% SBRs coexisting in triad genes, suggesting that CRE variations are critical for subgenome differentiations. Knocking out of TaSPL7A/B/D and TaSPL15A/B/D subfamily further proved that both high- and low-affinity SBRs played critical roles in the differential expression of genes regulating tiller number and spike sizes. Our results have provided baseline data for downstream networks of SPLs and wheat improvements and revealed that CRE variations are critical sources for subgenome divergence in the allohexaploid wheat.

2022-11-28 | GSE188699 | GEO

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq]

2022-11-28 | GSE188723 | GEO

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [ATAC-seq]

2022-11-28 | GSE188696 | GEO

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

Project description:Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

| PRJNA779995 | ENA

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [ATAC-seq]

Project description:Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [ATAC-seq]

| PRJNA779945 | ENA

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [DAP-seq]

Project description:Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [DAP-seq]

| PRJNA779959 | ENA

Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat

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

2022-11-28 | GSE188724 | 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

Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression

Project description:Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely-cultivated allohexaploid wheat variety carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.

2020-11-30 | GSE139020 | GEO

Distinct chromatin signitures of promoters, enhancers and transposons in allohexaploid wheat

Project description:Bread wheat is allohexaploid with 16 Gb genome, which has large intergenic region with abundant TEs and regulatory sequences . Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide the first systematic epigenomic map for functional annotation of the allohexaploid wheat genome.

2019-06-21 | GSE121903 | GEO

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