NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE167228 Query DataSets for GSE167228
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)
GSM5100020 G1812_ChIPseq_H3K27me3
GSM5100021 G1812_ChIPseq_H3K27me3_ABA
GSM5100022 G1812_ChIPseq_H3K9ac
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

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE167228_G1812_all_treatment.fpkm.txt.gz 1.6 Mb (ftp)(http) TXT
GSE167228_RAW.tar 9.2 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap