Analysis and Annotation of DNA Methylation in Two Nonhuman Primate Species Using the Infinium Human Methylation 450K and EPIC BeadChips

Abstract

Aim: Nonhuman primates are essential for research on many human diseases. The Infinium Human Methylation450/EPIC BeadChips are popular tools for the study of the methylation state across the human genome at affordable cost. Methods: We performed a precise evaluation and re-annotation of the BeadChip probes for the analysis of genome-wide DNA methylation patterns in rhesus macaques and African green monkeys through in silico analyses combined with functional validation by pyrosequencing. Results: Up to 165,847 of the 450K and 261,545 probes of the EPIC BeadChip can be reliably used. The annotation files are provided in a format compatible with a variety of standard bioinformatic pipelines. Conclusion: Our study will facilitate high-throughput DNA methylation analyses in Macaca mulatta and Chlorocebus sabaeus.

Prenatal delta-9-tetrahydrocannabinol exposure is associated with changes in rhesus macaque DNA methylation enriched for autism genes

“…Stratified quantile normalization preprocessing was performed using minfi to adjust for probe-type bias in beta distributions. Probes previously determined to be functional and valid in Macaca mulatta (referred to as MM_valid) [ 48 ] were retained prior to removing probes with failed detection p value > 0.01 in ≥ 25% of samples. For each tissue, we visually inspected the median intensity of measurements on the X and Y chromosome and confirmed that predicted sex agreed with biological sex.…”

“…Heart DNA was not available for one THC-exposed animal, and one cerebellum dataset (CON) was removed following quality control analysis due to low intensity. After quantile normalization and retaining probes previously validated in Macaca mulatta [48], we observed clear separation of datasets by tissue (Additional file 1: Figure S1).…”

DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

“…Despite the extraordinary contribution of Infinium arrays to human DNA methylation studies, there have been no equivalent commercial arrays targeting any model organism developed to date. There have been sporadic attempts to apply the human Infinium arrays to primates (Housman et al, 2018; Housman et al, 2020; Nakachi et al, 2020; Pichon et al, 2021) and mice (Gujar et al, 2018; Needhamsen et al, 2017; Wong et al, 2013). However, only 1% of Infinium Methylation EPIC probes are mappable to the mouse genome, which can lead to array scanning problems, in addition to the cost inefficiency and poor content utilization.…”

Value of methylation markers in colorectal cancer (Review)

“…DNA methylation can be detected using a variety of methods, such as methylation-specific polymerase chain reaction (15), DNA sequencing, MethyLight (16), methylation-specific melting curve analysis (17), pyrosequencing (18), microarray analysis (19) and liquid chromatography (LC). Notably, LC was the first platform used to quantify global DNA methylation, which was represented by the total 5-methyldeoxycytidine content in DNA samples (20).…”