ADPr-Seq analysis software: a novel approach for genome-wide quantification and differential binding analysis of ADP-ribosylated DNA

(2025) ADPr-Seq analysis software: a novel approach for genome-wide quantification and differential binding analysis of ADP-ribosylated DNA. Gitlab [Software]

Record type: Software

Abstract

ADP-Ribosylation (ADPr) is a recently discovered DNA-modification found in prokaryotes and more recently in eukaryotes. This modification is involved in the dynamic regulation of cell-cycle, DNA-replication and repair, and may play a role in mutagenesis. Its role in many organisms has yet to be elucidated.

Currently there is no published high throughput genome-wide method and bioinformatics pipeline to profile ADPr sites in DNA. As this modification is labile, high-energy methods for DNA shearing (e.g. sonication) used in traditional chromatin immuno-precipitation (IP) followed by sequencing (ChIP-Seq) fails to yield optimally enriched precipitates and therefore are not applicable.

Here we describe a method based on reproducible restriction enzyme DNA fragmentation and immuno-precipitation of ADP-ribosylated nucleotides followed by sequencing (ADPr-Seq). As the enzymatic fragmentation generates reproducible DNA fragments with known start and end positions in the organism genome, ADPr-Seq allows direct fragment quantification, obviating the need for peak-calling or window-based counting. Our new approach simplifies identifying differentially bound regions by eliminating the need to harmonize the start and end locations of each peak across replicates and conditions.

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