Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources

Cytosine methylation, a crucial epigenetic modification, plays a vital role in genomic regulation. Leveraging the advancements in long-read sequencing, we investigate the methylation patterns of polymorphic transposable element (TE) insertions of human lymphoblastoid cell lines (LCLs). We validate the high concordance between long-read methylation calls and the conventional whole-genome bisulfite sequencing (WGBS) method. We then aim to establish general rules of TE methylation with our data by addressing three key questions: (1) what is the methylation profile of each insertion; (2) do newly inserted TEs adopt the methylation pattern of their genomic context; and (3) do new TE insertions affect the methylation of their flanking regions. Although most non-TE insertions exhibit DNA methylation patterns consistent with their genomic context, TE insertions are generally highly methylated, exhibiting distinct, class-specific patterns with some variation within TE bodies. A small percentage of Alu insertions are hypomethylated, particularly those inserted within hypomethylated CpG islands. We also reveal that majority of TEs exhibited minimal impact on nearby regions, although numerous exceptions exist in which the methylation status of TEs spread into nearby regions. In conclusion, although TE insertions primarily exhibit methylation patterns restricted within their boundaries, some TEs are able to affect the methylation level of their genomic neighborhoods. At last, our findings are limited to human LCLs, and more comprehensive analysis would be needed to test the rules we found here on a broader spectrum of cell types and developmental stages.