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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

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Modbed track: Visualization of modified bases in single-molecule sequencing.

Daofeng Li¹, Xiaoyu Zhuo¹, Jessica K Harrison¹

¹Department of Genetics, The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.

|December 20, 2023

Summary

New visualization tools enable researchers to explore epigenome data from long-read sequencing. The modbed track type in the WashU Epigenome Browser displays chemical modifications on DNA bases within individual reads.

Keywords:

WashU Epigenome Browser long-read sequencing methylation visualization

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Area of Science:

Genomics and Epigenetics
Bioinformatics and Computational Biology

Background:

Long-read sequencing technologies have advanced significantly, improving read length and accuracy in detecting DNA base modifications.
Investigating the epigenome is crucial for understanding gene regulation, but visualization of modified bases in genome browsers remains a challenge.

Purpose of the Study:

To address the limitations in visualizing modified bases from long-read sequencing data.
To introduce a novel track type for enhanced exploration of epigenomic information.

Main Methods:

Development and implementation of the 'modbed' track type within the WashU Epigenome Browser.
The modbed track visualizes modification details at single-read and aggregated molecule levels across various resolutions.
Support for local file uploads and accessible URLs for seamless data integration.

Main Results:

The modbed track type successfully enables visualization of chemical modifications on canonical nucleotide bases from long-read sequencing data.
Users can now explore detailed modification patterns within individual sequencing reads and across multiple molecules.
The WashU Epigenome Browser provides a platform for dynamic and high-resolution epigenomic data visualization.

Conclusions:

The modbed track type significantly enhances the ability to visualize and analyze epigenomic data generated by long-read sequencing.
This advancement facilitates a more comprehensive exploration of the epigenome, opening new avenues for biological discovery.
The WashU Epigenome Browser offers a free and accessible tool for researchers studying DNA modifications.