Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments

Abstract

Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often overlooked by computing average methylation levels at CpG sites. In this study, to facilitate the application of the DNA methylation heterogeneity measures in downstream epigenomic analyses, we present a Rust-based, extremely fast and lightweight bioinformatics toolkit called Metheor. Here, we benchmark the performance of Metheor against existing code implementation for DNA methylation heterogeneity measures in three different scenarios of simulated bisulfite sequencing datasets. Metheor was shown to dramatically reduce the execution time up to 300-fold and memory footprint up to 60-fold, while producing the same results with the original implementation. Source code for Metheor is at https://github.com/dohlee/metheor and is freely available for non-commercial users.

Methylation entropy landscape of Chinese long‐lived individuals reveals lower epigenetic noise related to human healthy aging

“…ME was calculated using DNA methylation entropy analysis software (DMEAS) (He et al., 2013). Referred to published study for methylation heterogeneity estimation tool development (Lee et al., 2023), we selected DNA segments with three consecutive CpGs, which were covered by at least five reads observed in at least half of the three groups (i.e., 40 in long‐lived individuals, 17 in younger controls, and 10 in elder controls). Here, Shannon entropy was calculated as follows:where b is the number of consecutive CpG sites in a segment (i.e., b = 3) and k is the number of observed methylation patterns in this segment (1 ≤ k ≤ 8); N is the total number of reads covering this segment and n i is the number of reads matching methylation pattern i (1 ≤ i ≤ N).…”

“…ME was calculated using DNA methylation entropy analysis software (DMEAS) (He et al, 2013). Referred to published study for methylation heterogeneity estimation tool development (Lee et al, 2023), we selected DNA segments with three consecutive CpGs, which were covered by at least five reads observed in at least half of the three groups (i.e., 40 in long-lived individuals, 17 in younger controls, and 10 in elder controls). Here, Shannon entropy was calculated as follows:…”

AMLs harboring DNMT3A-destabilizing variants show increased intratumor DNA methylation heterogeneity at bivalent chromatin domains

“…Since the oligomeric state of DNMT3A was shown to be dependent on the intracellular concentration of the protein 15 , we hypothesized that the distributive de novo methylation mediated by dimeric DNMT3A will be prevalent in DNMT3A INS AMLs. To quantify the extent of the processive or distributive de novo methylation from the traces left on the methylomes of AML patients, we utilized a computational measure called local pairwise methylation discordance 16 (LPMD; Figure 1b).…”

“…Through the enumeration of all the sequencing reads, LPMDd is computed as the proportion of CpG pairs at genomic distance 𝑑 (in bp) with different methylation states. LPMD values were computed using Metheor v0.1.2 16 .…”