Integrated genotyping, annotation and epigenetic characterization of transposable elements with GraffiTE

GraffiTE v1.1 genotypes SVs, annotates polymorphic mobile elements, and maps LRS-based CpG methylation, enabling allele-specific TE epigenetic characterization in 20 Quebec French-Canadian genomes.

• Why it matters: Long-read sequencing can measure CpG methylation, but existing TE genotyping tools discard allele-specific epigenetic information, limiting how TE variation is linked to epigenome regulation.
• What they did: The Nextflow pipeline integrates SV genotyping, MEI annotation, and epigenetic mapping via pangenome graphs, supporting LRS stencil–based methylation data including Fiber-seq. It was applied to genomes and methylomes from 20 Quebec residents of French-Canadian descent.
• The result: TE annotation identified 4,908 Alu, 704 LINE1, 112 SVA, and 21 HERVK (HML-2) polymorphic MEIs, adding 144,748 CpGs versus the reference; 480 Alus, 67 LINE1s, 12 SVAs, and 2 HERVKs were hypomethylated. MEI methylation shows a moderate age-linked demethylating effect (effect: -0.069 log-odds per log10 years, P < 6.08 x 10-19), with LINE1 expected to drop from 86.4% to 80.8% in the first Mya.

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