An Improved EMSA-based Method to Prioritize Candidate cis-REs for Further Functional Validation.
Bio-Protocol
|July 8, 2022
Summary
Regulatory element-sequencing (Reel-seq) is a new high-throughput method for precisely identifying gene regulatory elements. This technique uses electrophoresis mobility shift assays to map cis-regulatory elements across large genomic regions efficiently.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Gene expression is regulated by cis-regulatory elements (cis-REs), making their identification crucial for understanding gene regulation.
- Current methods for cis-RE identification can be limited in resolution, throughput, or scope.
Purpose of the Study:
- To introduce a novel, high-throughput, and high-resolution method for fine-mapping cis-regulatory elements.
- To provide a time-effective protocol for identifying cis-REs across large genomic regions.
Main Methods:
- Development of regulatory element-sequencing (Reel-seq), an in vitro, high-throughput technique.
- Utilizing electrophoresis mobility shift assay (EMSA) for cis-RE identification.
- Application of Reel-seq for systematic and continuous mapping of cis-REs.
Main Results:
- Reel-seq enables high-resolution and sensitive identification of cis-REs.
- The method is applicable to large genome regions.
- Reel-seq can prioritize candidate cis-REs effectively.
Conclusions:
- Reel-seq is a valuable addition to existing methods like MPRA, ChIP-seq, and ATAC-seq for cis-RE discovery.
- This technique offers a simple, time-effective, and systematic approach to decipher gene expression regulation mechanisms.
