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Identifying transcription start sites and active enhancer elements using BruUV-seq.

Brian Magnuson¹, Artur Veloso^1,2, Killeen S Kirkconnell^1,3

¹Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Scientific Reports

|December 15, 2015

Summary

This summary is machine-generated.

BruUV-seq uses UV light to map transcription start sites (TSSs) and enhancer RNAs genome-wide. This method enhances nascent RNA signals, improving the identification of active regulatory elements in cells.

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Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Identifying transcription start sites (TSSs) and enhancer elements is crucial for understanding gene regulation.
Existing methods for mapping nascent RNA and regulatory elements have limitations in resolution and scope.

Purpose of the Study:

To introduce a novel method, BruUV-seq, for genome-wide identification of TSSs and active enhancer elements.
To enhance the detection of nascent RNA and unstable transcripts.

Main Methods:

BruUV-seq involves UV light-induced DNA lesions to block transcription elongation before bromouridine labeling and deep sequencing.
This technique enriches nascent RNA signal at the 5'-end of genes and stabilizes transcripts associated with arrested RNA polymerases.

Main Results:

BruUV-seq accurately identifies TSSs by redistributing transcription reads towards gene 5'-ends.
The method significantly increases the signal for unstable transcripts, including putative enhancer RNAs (eRNAs).
Validation against GRO-cap demonstrated high overlap of BruUV-seq peaks with TSSs and enhancer elements, including TNF-induced elements.

Conclusions:

BruUV-seq is a powerful new approach for genome-wide identification of TSSs and active enhancer elements in intact cells.
This method facilitates the discovery of regulatory elements and their response to stimuli like TNF.