A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels
Abstract
5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) regulate gene expression and exhibit dynamic levels during development and disease. While high-depth, base-resolution studies offer the most detailed view of epigenetic landscapes, many open questions are answered by surveying changes in 5mC/5hmC levels across larger cohorts. Nonetheless, current global quantification methods, including mass spectrometry, are typically limited in accessibility, accuracy, or throughput. Here, to evaluate the viability of low-coverage sequencing as an alternative, we first computationally downsampled deeply sequenced data to resolve the three-way relationship between sequencing coverage, modification levels, and measurement error. This relationship allowed us to develop a facile online tool for error calculation and to define experimental targets:
Fields of Study & Subjects
Bacteriophages and microbial interactions
RNA modifications and cancer
CRISPR and Genetic Engineering
Publication details
- Journal / source
- NAR Genomics and Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Volume
- 8
- Issue
- 3
- Pages
- lqag082–lqag082
- Publication date
- 27 June 2026
- Language
- EN