Systematic mapping of functional enhancer-promoter connections with CRISPR interference

Area of Science:

• Genomics and Molecular Biology
• Epigenetics and Gene Regulation

Background:

• Mammalian gene expression relies on noncoding elements, but their functions and target genes are largely unknown.
• Understanding these elements is crucial for deciphering physiological processes and disease mechanisms.

Purpose of the Study:

• To develop and apply a high-throughput CRISPR interference (CRISPRi) approach for discovering gene regulatory elements and identifying their target genes.
• To investigate regulatory elements near the essential transcription factors MYC and GATA1.

Main Methods:

• Utilized clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) for high-throughput screening.
• Assessed over 1 megabase of sequence in the vicinity of MYC and GATA1.
• Analyzed chromatin state and chromosome conformation data.

Main Results:

• Identified nine distal enhancers that regulate gene expression and cellular proliferation.
• Seven enhancers were found to regulate MYC, distinguished by quantitative chromatin features.
• Developed a strategy for predicting enhancer-promoter connectivity based on chromatin and conformation data.

Conclusions:

• The CRISPRi-based approach is effective for discovering regulatory elements and their target genes.
• This method can dissect complex transcriptional networks.
• It offers a way to interpret the role of noncoding genetic variation in human diseases.