Integrated analysis of ribosomal DNA copy number and methylation using nanopore long-read sequencing

06 Jul 20264 min read0 viewsVerified Feed

GIST (Key Takeaways)

Ribosomal RNA (rRNA) provides the structural and catalytic core of ribosomes and is encoded by ribosomal RNA genes (rDNA) arranged in tandem repeat arrays. rDNA copy number (CN) is highly dynamic, representing a clinically relevant form of structural variation, but its accurate quantification has been challenging due to its highly repetitive and GC-rich nature.
Here, we present RICO (Ribosomal DNA Integrated Copy Number and Methylation Analysis), a novel computational pipeline for integrated estimation of rDNA CN and methylation using nanopore long-read sequencing. RICO leverages long sequencing reads that span entire rDNA repeats, mapped to an rDNA-augmented reference genome, and normalizes coverage using an array of single-copy genes.
We show that RICO provides accurate rDNA CN estimates in simulated datasets and reproducible measurements across human samples, with strong agreement to short-read sequencing and PCR-based methods.