CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences

Abstract

Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL’s performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL’s capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.

A comprehensive analysis of library preparation methods shows high heterogeneity of extrachromosomal circular DNA but distinct chromosomal amount levels reflecting different cell states

“…Subsequently, we analyzed the nanopore sequencing data using the CReSIL 37 tool for further comparison. Results showed that the number of eccDNAs identified by the CReSIL tool was significantly increased (Table S5†).…”

'A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS'

“…For a re ned understanding of the eccDNA source mechanisms, analysis pipelines that resolve complex eccDNA composites from multiple break events are necessitated. Applying such advanced technologies, Wanchai and colleagues recently suggested that only 1-2% of the circles in murine cortical tissue comprise a complex, multi-locular genomic origin [102]. Accounting for the suggested capability to embed pathophysiologically impactful sequences, in analogy to the recently described regulator and enhancer functions of long ecDNAs in tumors [47], the modes of interaction with the linear genome will greatly broaden our understanding of small eccDNA in the context of neurological disorders.…”

A review of strategies used to identify transposition events in plant genomes

“…Although the method was developed for identification and characterization of plant virus genomes, and includes the ‘annotate’ module that is restricted to viruses annotation, part of the pipeline that outputs eccDNA candidates and their genomic localization can be used for the identification of LTR-RTs. Other long-reads based tools, such as CReCIL ( Wanchai et al., 2022 ) allow not only efficient identification of circular DNA but also annotation and Circos-based visualization of assembled circles, but its performance was tested only on long-reads from mammals eccDNA sequencing. Another tool, ecc_finder ( Zhang et al., 2021 ) is based on a pipeline applied for the analysis of Mobilome-seq data originated from plant tissues ( Lanciano et al., 2017 ).…”