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Engreitz Lab

Summary

The Engreitz Lab is a computational and experimental genomics research group led by Jesse M. Engreitz at the Stanford University School of Medicine. The lab focuses on mapping the regulatory wiring of the human genome to understand how genetic variation contributes to complex human diseases. Their work combines high-throughput CRISPR perturbation screens (such as CRISPRi-FlowFISH) with predictive machine learning models to link enhancers to their target genes.

Research Focus

  • Enhancer-Gene Regulatory Maps: The lab is dedicated to mapping physical and functional connections between enhancers and promoters across various human tissues and cell types.
  • Predictive Modeling: Developing computational methods to predict enhancer-promoter communication, notably the Activity-by-Contact (ABC) Model and the supervised ENCODE-rE2G classifier.
  • CRISPR Screens: Implementing and scaling single-cell and pooled genetic perturbation assays (e.g. CRISPRi-FlowFISH and TAP-seq) to validate regulatory predictions and investigate enhancer synergy.
  • Variant Interpretation: Applying regulatory maps to identify causal variants, cell types, and target genes for common complex diseases studied in genome-wide association studies (GWAS).

Key Software and Models

  • Activity-by-Contact (ABC) Model: A mathematical model of enhancer-promoter regulation based on chromatin activity and 3D contact frequency.
  • ENCODE-rE2G: A supervised model predicting enhancer-gene connections by combining epigenomic data and CRISPR perturbation benchmarks.

See Also

Citations