Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Abstract

Repetitive elements, mostly derived from transposable elements (TEs), account for half the DNA in human and other mammalian genomes. Although epigenetic mechanisms, including DNA methylation and repressive histone modifications, have evolved to suppress TE activities, TEs have substantially shaped the regulatory landscape of the host genome by contributing regulatory sequences to it. TE-derived sequences are often highly repetitive and thus have low mappability, making it difficult to profile the genomics of TEs using short-read sequencing technology. Many specialized bioinformatics tools have been developed for TE-related analysis, but meaningfully visualizing, navigating, and interpreting such data remains challenging. Here, we describe the WashU Repeat Browser to host genomics profiles of human and mouse TEs using data produced by the ENCODE Project and to support the navigation, interactive visualization, integration, comparison, and analysis in the context of TEs. WashU Repeat Browser is a web-based platform allowing users to browse genomic and statistical signals over repetitive elements derived from ENCODE, Roadmap, and FANTOM datasets. The Browser provides a TE-centric view including TE subfamily enrichments, TE subfamily profiling, as well as overviews of genomic signals on individual TE loci where we extend the WashU Epigenome Browser to display user-selected datasets and TE loci. These features could help to close the gaps in our understanding of the repetitive sequences and their putative regulatory functions and aid investigators in formulating new hypotheses by integrating their data with public data.