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Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway
Tinyi Chu1, Zhong Wang1, Shao-Pei Chou1
1Baker Institute for Animal Health, Cornell University, Ithaca, New York.
Current Protocols in Bioinformatics
|December 28, 2018
Summary
dREG identifies active transcriptional regulatory elements (enhancers and promoters) using RNA polymerase data from sequencing assays. This protocol details how to run dREG on your own datasets to find regulatory elements and predict gene targets.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Transcription is a key chromatin mark for identifying active enhancers and promoters, known as transcriptional regulatory elements (TREs).
- Run-on and sequencing (RO-seq) assays like GRO-seq, PRO-seq, and ChRO-seq capture active transcription sites.
- Identifying TREs is crucial for understanding gene regulation and cellular responses.
Purpose of the Study:
- To provide a detailed protocol for running the dREG tool on arbitrary RO-seq datasets.
- To enable researchers to identify active transcriptional regulatory elements (TREs) using their own sequencing data.
- To demonstrate the application of dREG-identified regions in discovering regulatory elements and predicting target genes.
Main Methods:
- Utilizing the dREG computational tool for analyzing RO-seq data.
- Inputting bigWig files representing RNA polymerase locations.
- dREG predicts active TREs by analyzing patterns in sequencing reads.
Main Results:
- dREG successfully identifies genomic regions as active TREs from various RO-seq datasets.
- The protocol provides step-by-step instructions for dREG implementation.
- Demonstrated use of dREG regions for identifying transcription factors and predicting target genes.
Conclusions:
- This protocol offers a comprehensive guide for applying dREG to diverse RO-seq data.
- dREG is a valuable tool for discovering and analyzing transcriptional regulatory elements.
- The method facilitates the study of gene regulation and transcription factor function.
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