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Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq

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Transposable Elements

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2607))

Abstract

By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5’ UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.

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Acknowledgments

This work was supported by the French government, through the Agence Nationale de la Recherche (Idex UCAJEDI, ANR-15-IDEX-01; Labex SIGNALIFE, ANR-11-LABX-0028-01; RETROMET, ANR-16-CE12-0020; ImpacTE, ANR-19-CE12-0032; ActiveLINE, ANR-21-CE12-0001), the Cancéropôle PACA (Projet Emergence), the Fondation pour la Recherche Médicale (FRM, DEQ20180339170), Inserm (GOLD cross-cutting program on genomic variability) and CNRS (GDR 3546). We are grateful to IRCAN genomic platform, Genomed. Equipment acquisition for IRCAN platforms was supported by FEDER, Région Provence Alpes Côte d’Azur, Canceropole PACA, Conseil Départemental 06, ITMO Cancer Aviesan (plan cancer) and Inserm.

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Correspondence to Claude Philippe or Gael Cristofari .

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Philippe, C., Cristofari, G. (2023). Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_8

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

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