High-throughput platform for functional characterization of promoter snps
A high-throughput platform utilizing TFBS maps and MPRA to predict and validate the functional effects of promoter SNPs across species. It integrates evolutionary conservation data and RNA-seq to prioritize variants and quantify their transcriptional impact.
Overview
This innovative platform leverages evolutionary conservation of transcription factor binding sites (TFBS) along with massively parallel reporter assays (MPRA) to functionally characterize promoter single-nucleotide polymorphisms (SNPs). By integrating multiDAP-seq data with RNA-seq analyses, the platform provides a predictive model for SNPs that impact gene expression. The scalable and transformation-free methodology facilitates its application across diverse plant species, enhancing genetic research and crop improvement efforts.
Technical specifications
- MultiDAP-seq Mapping: Utilizes pooled genomic DNA from multiple species to identify conserved TFBSs.
- Integration with RNA-seq: Combines bulk and single-cell RNA-seq to map cis-regulatory elements at tissue and cell-type resolution.
- MPRA Implementation: Designed for Arabidopsis protoplasts, allowing high-throughput quantification of transcriptional effects of promoter variants.
- Broad Applicability: The method is transformation-free and can be applied to various species beyond Arabidopsis, including rice and tomato.
Technology readiness level
The current technology readiness level is 3, indicating that the platform has been validated in a laboratory setting with ongoing plans to expand its application to other species and test larger variant sets. The platform aims to establish a predictive system for validating regulatory SNPs efficiently.
About University of Chicago
The University of Chicago is a private institution that brings together the power of 140 institutes and centers including an NCI-designated Comprehensive Cancer Center, a microbiome focused center, two U.S. Department of Energy National Labs (Argonne National Laboratory and Fermi National Accelerator Laboratory) and the Marine Biological Laboratory, making it a truly powerful research and development enterprise of over 15,000 faculty and research staff. UChicago is home to the Pritzker School of Molecular Engineering, launched in 2011 as the first and only engineering school in the U.S. focused entirely on molecular engineering with one of the major focused areas in immunoengineering, and a core partner of the Chan Zuckerberg (CZ) Biohub - Chicago. Researchers at UChicago have pioneered breakthroughs including discovering the link between cancer and genetics, establishing revolutionary theories of economics, and developing tools to enhance urban schooling. UChicago researchers are at the forefront of fields ranging from quantum computing, data science and artificial intelligence, to the modeling and synthesis of advanced materials, to oncology and neuroscience.
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