|
| Status |
Public on Aug 31, 2021 |
| Title |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements I |
| Organism |
Triticum urartu |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
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.
|
| |
|
| Overall design |
In order to delineate the major TF regulatory circuitry to abiotic stresses in Triticum Urartu, we performed DAP-seq to obtain a genome-wide binding profile of stress response TFs, ChIP-seq for three well-studied histone modifications (including H3K9ac, H3K4me3 and H3K27me3), DNase-seq, Bisulphite-seq and RNA-seq in 5 stresses.
|
| |
|
| Contributor(s) |
Zhang Y |
| Citation(s) |
34503979 |
| |
| Submission date |
Feb 22, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
yijing zhang |
| E-mail(s) |
zhangyijing@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Biochemistry
|
| Lab |
Functional Epigenomics Group
|
| Street address |
2005 Songhu Road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platforms (2) |
| GPL29754 |
Illumina NovaSeq 6000 (Triticum urartu) |
| GPL29755 |
HiSeq X Ten (Triticum urartu) |
|
| Samples (25)
|
|
| This SubSeries is part of SuperSeries: |
| GSE167229 |
Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements |
|
| Relations |
| BioProject |
PRJNA703956 |
| SRA |
SRP307514 |
Less...
More...