Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq.
Bisulfite sequencing
DNA methylation
Epigenetics
L1
LINE-1
Methyl-cytosine
Retrotransposon
Transposable element
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
30
11
2022
pubmed:
1
12
2022
medline:
3
12
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 36449162
doi: 10.1007/978-1-0716-2883-6_8
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
127-150Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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