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Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (RNA-seq)

ABSTRACT: In this study, we employed RNA-seq to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE260872 | GEO | 2024/11/21

REPOSITORIES: GEO

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Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (ATAC-seq)

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Identify the interplay between N6-methyladenine and gene regulation under hypoxia by randomized empirical model (6mA)

Project description:This dataset encompasses comprehensive analyses of the epigenetic mark N6-methyladenine (6mA) in human cell lines, focusing on its role under hypoxic conditions and its association with cancer progression. Addressing the challenge of 6mA's low abundance in mammals, we have innovated the 6mA-ChIP-exo-5.1 method. This technique enhances the sensitivity and accuracy of 6mA detection, employing exonuclease-dependent antibody-based approaches combined with whole genome amplification (WGA) to minimize potential noise and false positives.

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Project description:To interrogate single-base resolution 6mA sites in the genome-wide, we develop DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an optimized sequencing method taking advantage of restriction enzyme DpnI, which exclusively cleaves methylated adenine sites. We find DpnI also recognizes other sequence motifs besides the canonical GATC restriction sites, largely expanding the application range of this method. DA-6mA-seq requires less starting material and lower sequencing depth than previous methods, but achieves higher sensitivity, providing a good strategy to identify 6mA in large genome with a low abundance of 6mA. We rebuild the 6mA maps of Chlamydomonas by DA-6mA-seq and then apply this method to another two eukaryotic organisms, Plasmodium and Penicillium. Further analysis reveals most 6mA sites are symmetric at various sequence contexts, suggesting 6mA may function as a new heritable epigenetic mark in eukaryotes. A new sequencing method is developed to detect 6mA in eukaryotes

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