DNA甲基化
生物
后转座子
遗传学
人类基因组
基因座(遗传学)
基因组
甲基化
亚硫酸氢盐测序
照明菌甲基化试验
基因
计算生物学
转座因子
基因表达
作者
Claude Philippe,Gaël Cristofari
出处
期刊:Methods in molecular biology
日期:2022-11-30
卷期号:: 127-150
被引量:3
标识
DOI:10.1007/978-1-0716-2883-6_8
摘要
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.
科研通智能强力驱动
Strongly Powered by AbleSci AI