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NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

ABSTRACT: NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

PROVIDER: PRJNA781728 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16978250_1.fastq.gz	Fastqsanger.gz
	SRR16978250_2.fastq.gz	Fastqsanger.gz
	SRR16978251_1.fastq.gz	Fastqsanger.gz
	SRR16978251_2.fastq.gz	Fastqsanger.gz
	SRR16978252_1.fastq.gz	Fastqsanger.gz

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NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Project description:Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

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NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule.

Project description:Cis-regulatory elements are coordinated to regulate the expression of their targeted genes. However, the joint measurement of cis-regulatory elements' activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single-nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

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Project description:Genomic sequences, as well as its covalent epigenetic modifications, are spatially organized into three-dimensional structures. Here, we developed Methyl-HiC by combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture genome-wide chromosome conformation changes and DNA methylation within the same DNA molecule. Methyl-HiC generated consistent information compared with in situ Hi-C and WGBS from the same cell line. We detected long-range DNA methylation concordance in general but varied in different chromatin states. We extended Methyl-HiC to single cell level and applied it on 103 primed and 47 naïve mouse embryonic stem cells (mESCs). We revealed the heterogeneity of chromosomal conformation changes by grouping cells in their DNA methylation level alone. We also observed increases of DNA methylation stochasticity and decreases of contact frequency together in late replication timing regions. Our method here paves the road to evaluate the direct long-range effect of epigenetic alterations in different pathological and healthy conditions at genome-wide and single cell level.

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Project description:DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions, that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule and thus, single cell level that can be used to monitor disease progression and response to therapy. Nucleosome Occupancy and Methylome-Sequencing (NOMe-Seq) on IMR90 cell line and 2 GBM cell lines

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