{
  "id": 19231913,
  "title": "Integrated genotyping, annotation and epigenetic characterization of transposable elements with GraffiTE",
  "url": "https://urgent.news/2026/11/09/integrated-genotyping-annotation-and-epigenetic-characterization-of",
  "topic": "science",
  "section": "Science",
  "published": "2026-11-09T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.11.06.764993v1?rss=1"
  },
  "original_language": "en",
  "account": "The introduction of GraffiTE v1.1 marks a significant advancement in genotyping, annotating, and characterizing transposable element (TE) variation, thanks to the capabilities of long-read sequencing (LRS) and de novo assembly techniques. LRS methods can reveal CpG methylation, which allows for assessing the influence of TEs on epigenomes and understanding the role of TEs as regulatory sequences. However, existing TE genotyping tools often disregard the valuable allele-specific epigenetic information.\n\nGraffiTE v1.1, a novel Nextflow pipeline, is presented as the first solution to address this limitation. It is designed to genotype structural variation (SV) events, annotate polymorphic mobile elements (MEI), and map epigenetic data to TEs using pangenome graphs – all in a single command. This pipeline is versatile and can accommodate various epigenetic information derived from LRS stencils, including Fiber-seq sequencing.\n\nTo showcase its prowess, GraffiTE v1.1 was applied to analyze genomes and methylomes obtained from 20 Quebec residents of French-Canadian descent. In these genomes, TE annotation revealed a total of 4,908 Alu, 704 LINE1, 112 SVA, and 21 HERVK (HML-2) distinct polymorphic mobile elements (MEIs). Furthermore, 10 fixed HERVK insertions were identified, varying between solo LTR and provirus, or in terms of proviral copy number.\n\nA noteworthy finding of the study is that these MEIs contribute to 144,748 additional CpGs not present in the reference genome. By analyzing the methylation status of these MEIs, the researchers determined that 480 Alus, 67 LINE1s, 12 SVAs, and 2 HERVKs were found in hypomethylated states. Interestingly, Alus and SVAs were found to be more heavily methylated than other LINE1 and HERVK elements.\n\nThe study also provides insights into the age of these MEIs, estimating their mean age to be 1.08 million years ago (with a median of 640 thousand years ago). A beta regression analysis revealed a moderate demethylating effect of age on MEIs, with each additional log10 year associated with an effect of -0.069 log-odds (P-value available).",
  "summary": "Genotyping, annotating and characterizing TE variation leaped forward with long-read sequencing (LRS) and de novo assembly. LRS techniques also reveal CpG methylation, which enables measuring the impact of TEs on epigenomes and sheds light on the role of TEs as regulatory sequences. Yet, TE genotyping tools discard the valuable allele-specific epigenetic information. We introduce GraffiTE v1.1,…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}