Single nucleotide variant analysis of promoters by sequencing (snap-seq) in plants
SNAP-seq is an innovative platform adapting STARR-seq to evaluate single nucleotide variants in plant promoters, enabling high-throughput screening for gene expression impact. Ideal for studying regulatory mechanisms in crops, it's validated in soybean systems.
Overview
The Single Nucleotide variant Analysis of Promoters by sequencing (SNAP-seq) is a cutting-edge platform designed to assess the impact of single nucleotide variants (SNVs) on plant promoters. By adapting the established STARR-seq method, SNAP-seq enables high-throughput screening of promoter variants in various plant systems, such as soybean hairy root composite systems. This approach is essential for understanding gene regulation, offering applications in developmental and stress-responsive studies across different crops.
Technical specifications
- Methodology: Utilizes synthetic promoter libraries with SNVs driving reporter gene expression.
- High-Throughput Screening: Barcoded reporters and saturated mutagenesis combined with next-generation sequencing identify SNVs affecting expression.
- Versatility: Applicable to different plant systems, including soybean, tobacco, and maize, using hairy root and transient gene expression systems.
- Validation: Successfully demonstrated in soybean hairy roots, and further applicable to other plant systems for studying specific stress responses.
Technology readiness level
SNAP-seq is currently at TRL 3, indicating experimental proof of concept has been achieved. Future validation plans include extending this method to other plant systems and using it to explore promoter variants under various stress conditions.
About South Dakota State University
South Dakota State University is a comprehensive public land‑grant research university serving a large statewide community. Industry engages through a university‑linked research and technology park that colocates tenant companies with faculty labs and pilot‑scale processing suites for de‑risking and demonstration. A statewide extension network and field sites provide real‑world environments for validation and market feedback, while shared‑use core facilities and tailored workforce pipelines connect talent and tools to corporate R&D. Research is supported by competitive federal funding from USDA and NSF, with additional awards from NIH and DOE, alongside state and industry partnerships. A dedicated technology transfer office manages IP and industry agreements, and incubator space at the research park supports startup formation and scale‑up.
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