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

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

PROVIDER: PRJNA703956 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13762850_1.fastq.gz	Fastqsanger.gz
	SRR13762850_2.fastq.gz	Fastqsanger.gz
	SRR13762851_1.fastq.gz	Fastqsanger.gz
	SRR13762851_2.fastq.gz	Fastqsanger.gz
	SRR13762852_1.fastq.gz	Fastqsanger.gz

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

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 [DAP-Seq]

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

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

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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

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

2021-08-30 | GSE167229 | GEO

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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Project description:Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE) might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes) a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes.

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