Methylation barriers are short DNA sequence segments that prevent methylation from spreading from repetitive elements to adjacent promoters. These sequence segments share common motifs recognized by transcription factors and subsequently alter the DNA methylation process.
The batch_lmer_topo_logit.r contains R functions that scan the human genome for differentially methylated promoter-CpG island-repeat (dmPIR) trios based on whole-genome bisulfite sequencing data (WGBS) or reduced-representation bisulfite sequencing (RRBS) data. These functions were used to produce results reported in our 2024 Nucleic Acid Research publication:
Jingmin Shu, Jaroslav Jelinek, Hai Chen, Yan Zhang, Taichun Qin, Ming Li, Li Liu, Jean-Pierre J Issa (2024) Genome-wide screening and functional validation of methylation barriers near promoters. Nucleic Acids Research. doi: 10.1093/nar/gkae302. Online ahead of print. PMID: 38647050