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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [DAP-Seq]

ABSTRACT: Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [DAP-Seq]

PROVIDER: PRJNA703960 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13762900_1.fastq.gz	Fastqsanger.gz
	SRR13762900_2.fastq.gz	Fastqsanger.gz
	SRR13762901_1.fastq.gz	Fastqsanger.gz
	SRR13762901_2.fastq.gz	Fastqsanger.gz
	SRR13762902_1.fastq.gz	Fastqsanger.gz

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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [DAP-Seq]

Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.

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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements I

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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements

Project description:Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements

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Project description:Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements I

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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [ChIP-Seq]

Project description:Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements [ChIP-Seq]

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Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements

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Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

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Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements.

Project description:More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

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