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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE260869 | 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 (RNA-seq)

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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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Project description:In this study, we employed ChIP-seq for histone modifications related to gene activation, such as H3K4me1, H3K4me3, and H3K27Ac, to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

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

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

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Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

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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N6-Methyladenine DNA Modification in Human Genome

Project description:In human cells, 5-methylcytosine (5mC) DNA modification plays an important role in gene regulation. However, N6-methyladenine (6mA) DNA modification, which is predominantly present in prokaryotes, is considered to be absent in human genomic DNA. Here, using single molecule real-time (SMRT) sequencing on human blood, we show that DNA 6mA modification is extensively present in human genome, accounting for ~0.051% of the total adenines. [G/C]AGG[C/T] was the most significant motif associated with 6mA modification. 6mA sites are enriched in the exon coding regions and are associated with transcriptional activation. DNA N6-methyladenine and N6-demethyladenine modification in human are mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The 6mA abundance is significantly lower in cancer tissues compared to adjacent normal tissues, which is accompanied with decreased N6AMT1 and increased ALKBH1 levels. Decrease of 6mA modification level stimulated tumorigenesis in human. Collectively, our results demonstrate that 6mA DNA modification is present in human tissues, and we describe a potential role of the N6AMT1/ALKBH1-6mA regulatory axis in the progression of human cancer.

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Project description:N6-methyladenine (6mA) is a natural DNA modification and functions primarily in restriction-modification (R-M) systems in prokaryotes. Recent studies uncovered the existence and revealed the genome-wide distribution of 6mA in eukaryotes. Specifically, it was reported that 6mA was mainly enriched in mammalian mitochondrial DNA (mtDNA) and could regulate mitochondrial activity. we achieved the genome-wide mapping of 6mA in E. coli genome and mammalian mtDNA at single-nucleotide resolution.

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Project description:N6-methyladenine (6mA) DNA modification in eukaryotic genomes has emerged as a potential epigenetic mark. However, little is known about how 6mA epigenetic codes are read and interpreted in higher eukaryotes. Here we investigate 6mA genome-wide distributions in multiple higher eukaryotes. Using Drosophila as a pioneer system, we show that 6mA exhibits defined patterns and preferentially marks zygotic genes in early embryos. Moreover, we identify that the Fox-family protein, Jumu, is a "6mA-DNA reader" and functions in concert with DMAD to contribute to zygotic gene activation. Further methylome analysis reveals that 6mA modification has common features in genomic DNA from mouse, rat and monkey, and that "forkhead-domain-binding motifs" are enriched in 6mA-marked DNA of these genomes, in a way similar to Drosophila. Collectively, our findings identify the 6mA DNA reader protein and suggest a conserved 6mA-based mechanism in higher eukaryotes.

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Active N6-Methyladenine demethylation by DMAD regulates gene expression by modulating the binding dynamics of Polycomb protein in neurons

Project description:A Ten-Eleven Translocation (TET) ortholog has been identified as a DNA N6-Methyladenine (6mA) demethylase (DMAD) in Drosophila. However, the molecular roles of 6mA and DMAD remain largely unexplored. Through genome-wide 6mA and transcriptome profiling, we found that 6mA may serve as a repressive epigenetic mark on a group of genes involved in neurodevelopment and neuronal functions. Mechanistically, DMAD coordinates with Trithorax-related complex protein Wds to maintain active transcription by dynamically demethylating intragenic 6mA. Accumulation of 6mA by depleting DMAD recruits Polycomb protein Pc as 6mA reader and contributes to transcriptional repression. Our findings define an epigenetic role for 6mA and suggest that active 6mA demethylation by DMAD plays important roles in fly CNS function by coordinating additional epigenetic mechanisms.

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