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| Status |
Public on Nov 08, 2023 |
| Title |
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis of chromatin accessibility in kidney bean under drought stress |
| Organism |
Phaseolus vulgaris |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: To identify nucleosome-depleted regions in response to drought in the kidney bean, a genome-wide chromatin profiling strategy was implemented. A better understanding of these OCRs (Open chromatin regions) will be useful in exploring potential genomic regions for crop improvement.
Results: Using a comprehensive FAIRE-Seq approach, nucleosome-free chromatin regions were explored in kidney bean (Phaseolus vulgaris. L) in response to both drought and rewatering stress. In all samples, FAIRE peaks (>50%) were enriched in the promoter regions. The drought samples showed peaks very distinct from control and rewatered samples, which showed peaks predominantly at the transcription start site (TSS). Drought and heat-responsive genes and transcription factors were identified within the flanking region of differential peaks. When drought was compared to control, it showed upregulated differential peaks primarily in the promoter and distal intergenic regions.
Conclusion: By analyzing FAIRE we are able to identify distinct genomic regions corresponding to droughts and controls. Upstream regions of genes play a significant role in drought stress response. Our data suggest that promoter regions of >2 kb, downstream regions of <= 300, and distant regulatory regions are predominant during the upregulation of drought stress. It would also be helpful to note that genomic regions vary in response to drought, and distal intergenic regions may also be involved in drought responses. Understanding plant genomes and epigenomics could help us develop varieties that can withstand extreme weather conditions.
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| Overall design |
Phaseolus vulgaris L. (Red Hawk dark red kidney bean) was exposed to drought stress at the R2 stage, when 50% of the flowers had opened. Plants were not watered until wilting occurred. Following 10 days, young leaves from three drought and control plants were randomly collected. An additional set of samples was collected ten days after irrigation of control and drought-stressed plants. The FAIRE-Seq was carried out on three biological replicates of each sample.
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| Contributor(s) |
Subramani M, Penny M, Lofton LW, Xie S, Florez CU, Moore M, Thimmapuram J, Kalavacharla V |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 02, 2021 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Shaojun Xie |
| E-mail(s) |
xie186@purdue.edu
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| Phone |
7657140672
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| Organization name |
Purdue University
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| Street address |
3135 Decatur Street
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| City |
WEST LAFAYETTE |
| State/province |
Indiana |
| ZIP/Postal code |
47906 |
| Country |
USA |
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| Platforms (1) |
| GPL24868 |
Illumina HiSeq 2500 (Phaseolus vulgaris) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA777286 |
| SRA |
SRP344272 |
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