Nanopore sequencing reveals hidden landscape of short L1 transductions in colorectal cancer

Abstract

L1s are repetitive sequences capable of copying themselves into new genomic loci. While L1s are typically repressed by DNA methylation in somatic tissues, they can become reactivated in cancer. Although L1 sequences are highly repetitive, ~25% of insertions carry a unique downstream sequence, transduction, that can be used to trace the source L1. Here, we apply nanopore long-read sequencing to 56 colorectal cancer samples to comprehensively detect somatic transductions and to characterize the source L1 activity. We demonstrate that earlier methods systematically miss a large proportion of mostly shorter transductions, leading to an incomplete and biased view of source L1 activity. Our analysis reveals a strong positive correlation between the number of transductions and other L1 insertions within samples and that distinct source L1s exhibit varying transduction lengths and 5' inversion frequency. Finally, we integrate DNA methylation provided by nanopore reads and show that active elements in cancer samples have lower methylation levels in contrast to inactive L1s. Together, our results provide a more complete characterization of somatically active L1 elements in colorectal cancer and highlight the utility of long-read sequencing in retrotransposon research.