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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Triticum urartu

PROVIDER: GSE167229 | GEO | 2021/08/30

REPOSITORIES: GEO

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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.

2021-08-31 | GSE167228 | GEO

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

2021-08-31 | GSE167227 | GEO

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

2021-08-31 | GSE182693 | GEO

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

| PRJNA703958 | ENA

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

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

| PRJNA703956 | ENA

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]

| PRJNA757431 | ENA

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]

| PRJNA703960 | ENA

Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements.

Project description:Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant Arabidopsis thaliana. We show that mutations in most of these exapted TEs result in phenotypes, particularly when challenged by abiotic stress. We built statistical multi-dimensional phenotypic profiles and compared them to wild-type and known stress responsive mutant lines for each particular stress condition. We found that these exapted TEs may play roles in responses to phosphate limitation, tolerance to high salt concentration, freezing temperatures, and arsenic toxicity. These results not only experimentally validate a large set of putative functional exapted TEs recently discovered through computational analysis, but also uncover additional novel phenotypes for previously well-characterized exapted TEs in A. thaliana.

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Transposable elements contribute to activation of maize genes in response to abiotic stress.

Project description:Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress, and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress-induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

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Abiotic stress-responsive expression of wali1 and wali5 genes from wheat.

Project description:Two cDNA clones, encoding Aluminum-responsive wali1 and wali5, were identified in dehydration stress-specific cDNA library from wheat. Their sequence variations and structural dissimilarities indicated them to be non-homologous genes. Expression of both genes was induced by various abiotic stresses as well as in response to plant hormones and oxidative molecules. Further, they were expressed differentially in shoot and root tissues of wheat seedlings, their transcripts being specifically abundant in roots. Previously characterized as being only Aluminum treatment induced, this report proposes them as novel candidates for stress-responsive studies.

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