Cis-regulatory SNP framework for enhanced crop promoter design
A platform that predicts gene activity changes due to SNPs in cis-regulatory modules, aiding rational promoter design for improved crop traits. Utilizes existing motif libraries and provides a gene-agnostic approach for enhanced expression and regulatory hotspot identification.
Overview
This innovative platform leverages the detection of cis-regulatory SNPs to predict changes in gene activity, offering a powerful tool for smarter crop design. By transforming motif recognition outputs onto a uniform scale called Expected Recognition Rate, this framework allows for the accurate prediction of promoter variants with enhanced expression capabilities. The platform is gene- and species-agnostic, ensuring wide applicability across various plant species and providing valuable insights for targeted genetic engineering and crop improvement.
Technical specifications
- Promoterome Modeling: Constructs Expected Recognition Rate tables for plant promoteromes using existing transcription factor binding site motifs, enabling precise modeling of promoter activity.
- SNP Impact Scoring: Maps SNPs from various sources onto composite cis-regulatory elements and scores their effects on promoter activity, facilitating the identification of regulatory hot spots.
- Framework Integration: Develops a universal computational pipeline that combines motif scoring, SNP impact prediction, and promoter variant ranking, streamlining the process of crop improvement.
- Proven Validation: Previous research has confirmed the efficacy of the tools used, including motif libraries and SNP effect modeling, minimizing risks and ensuring reliable results.
Technology readiness level
This platform is at Technology Readiness Level 3, indicating that it has been demonstrated in a controlled research environment. Further development and validation in practical applications are planned to advance its readiness.
About Radboud Universiteit
Radboud University is a large, comprehensive public research university in Nijmegen, the Netherlands, with a broad academic profile and a strong culture of interdisciplinary collaboration. Its campus is closely integrated with Radboudumc, linking academic research, clinical expertise, and translational pathways. Companies can engage through research facilities and equipment, commissioned research, consortium projects, and the Nijmegen Science Park within the wider Lifeport innovation network. Research draws on competitive national and European funding, including NWO, ZonMw, and Horizon Europe. Knowledge-transfer support helps develop partnerships, protect intellectual property, license results, and form spin-offs.
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