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Genome-wide quantitative enhancer activity maps identified by STARR-seq.

Cosmas D Arnold¹, Daniel Gerlach, Christoph Stelzer

¹Research Institute of Molecular Pathology (IMP), Vienna, Austria.

Science (New York, N.Y.)

|January 19, 2013

Summary

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Scientists developed STARR-seq, a new method to directly measure the activity of millions of genomic enhancers. This powerful tool creates comprehensive enhancer maps and reveals complex gene regulation across entire genomes.

Area of Science:

Genomics
Molecular Biology
Gene Regulation

Background:

Genomic enhancers control gene expression but are difficult to identify using indirect methods.
Current techniques lack the ability to directly and quantitatively assess enhancer activity on a large scale.

Purpose of the Study:

To develop a novel method for direct and quantitative assessment of enhancer activity.
To enable genome-wide screens for identifying and characterizing enhancers.

Main Methods:

Developed STARR-seq (Self-Transcribing Activated Regulatory Region sequencing) to directly measure enhancer activity.
Applied STARR-seq to the Drosophila genome to screen millions of DNA candidates.
Quantitatively assessed enhancer activity across a broad spectrum of strengths.

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Main Results:

Identified thousands of cell type-specific enhancers in Drosophila.
Linked differences in gene expression directly to variations in enhancer activity.
Generated a genome-wide quantitative map of enhancers, revealing complex transcriptional regulation.
Observed multiple independent enhancers regulating both developmental and ubiquitous genes.

Conclusions:

STARR-seq provides a direct, quantitative, and scalable method for enhancer identification and activity assessment.
The developed enhancer map offers insights into the intricate mechanisms of gene regulation.
STARR-seq is applicable to diverse eukaryotic systems, including humans, for enhancer research.