ECCsplorer: detection of extrachromosomal circular DNA (eccDNA) from NGS data
Creators: name: Mann, Ludwig
name: Seibt, Kathrin M.
name: Weber, Beatrice
name: Heitkam, Tony
Publisher: name: Zenodo
Year: 2020
Subjects: eccDNA
extrachromosomal circular DNA
circDNA
circSeq
TE activity
bioinformatics
pipeline
mobilome
ECCsplorer

description: Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes. They have been reported in a broad range of eukaryotes ranging from around 100 bp to several megabasepairs in size. Although most of their functions still remain unknown, some eccDNAs are associated with stress, cancer or aging, some carry gene copies, and some harbor repetitive DNAs. Other studies also reported active retrotransposons forming circular products besides of reintegrating into the genome. Therefore, eccDNAs can act as a crucial hint for detecting unknown transposon activity. Here, we present the ECCsplorer, a bioinformatics pipeline to detect eccDNAs in any kind of organism or tissue using next-generation sequencing techniques. Amplified circular DNA serves as initial input for sequencing (circSeq) and an easy, automated and unified discovery of eccDNA candidates. The approach is based on two major procedures: Firstly, read mapping to the reference genome is followed by detection of exceptional read distributions including high coverage, discordant mapping and split reads. Secondly, reference-free comparison of read clusters from amplified eccDNA with control sample data reveals specific enrichment of circles. Both parts can be run separately or combined depending on the individual aim or data availability. ECCsplorer further provides compelling, ready-to-use visualizations of the eccDNA fractions. To illustrate our approach, we re-analyzed published Arabidopsis and human eccDNA data, confirming the sensitivity and specificity of our pipeline for the identification of TE mobilization. To investigate the tool’s performance for the detection of known circular DNA populations, we further selected the crop plant sugar beet, reported to contain a variety of mitochondrial mini-circles not present on the published reference genome. For all samples, ECCsplorer comprehensively detected enriched eccDNAs with high accuracy and precision. Especially for the analysis of transposon activity, our tool provides an easy to apply bioinformatics solution to tackle the growing amount of eccDNA-related research questions.
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