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Methyl-ATAC-seq measures DNA methylation at accessible chromatin

ABSTRACT: methyl-ATAC-seq measures DNA methylation at accessible chromatin

PROVIDER: PRJNA521336 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8544480.fastq.gz	Fastqsanger.gz
	SRR8544490.fastq.gz	Fastqsanger.gz
	SRR8544481.fastq.gz	Fastqsanger.gz
	SRR8544491.fastq.gz	Fastqsanger.gz
	SRR8544482.fastq.gz	Fastqsanger.gz

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methyl-ATAC-seq measures DNA methylation at accessible chromatin

Project description:Here we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin, and reveals the DNA methylation state of the underlying DNA.

2019-02-08 | GSE126215 | GEO

methyl-ATAC-seq measures DNA methylation at accessible chromatin.

Project description:Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA. For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying data sets. Here, we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, including subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin and reveals, unambiguously, the DNA methylation state of the underlying DNA. Such combinatorial methods eliminate the need to perform assays independently and infer where features are coincident.

| S-EPMC6581052 | biostudies-literature

The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)

Project description:In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.

2016-06-15 | E-GEOD-66581 | biostudies-arrayexpress

ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome

Project description:ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome

| PRJNA533829 | ENA

3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome

Project description:Spatial genome organization is essential to direct fundamental DNA-templated biological processes (e.g. transcription, replication, and repair), but the 3D in situ nanometer-scale structure of accessible cis-regulatory DNA elements within the crowded nuclear environment remains elusive. Here, we combined the recently developed Assay for Transposase-Accessible Chromatin with visualization (ATAC-see), PALM super-resolution imaging and lattice light-sheet microscope (a method termed 3D ATAC-PALM) to selectively image and quantitatively analyze key features of the 3D accessible genome in single cells. 3D ATAC-PALM reveals that accessible chromatin are non-homogeneously organized into spatially segregated clusters or accessible chromatin domains (ACDs). To directly link imaging and genomic data, we optimized multiplexed imaging of 3D ATAC-PALM with Oligopaint DNA-FISH, RNA-FISH and protein fluorescence. We found that ACDs colocalize with active chromatin and enclose transcribed genes. By applying these methods to analyze genetically purterbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight the 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.

2020-01-29 | GSE126112 | GEO

Genomic and epigenomic study of Japanese renal cell carcinoma including WGS, RNA-seq, ATAC-seq, and methyl-seq

Project description:We performed whole-genomic and transcriptomic sequencing of more than 100 Japanese renal cell carcinoma (RCC) cases, including clear cell RCC, papillary RCC, chromophobe RCC, and TFE3-translocated RCC. In addition, we conducted epigenome sequencing analyses: the assay for transposase-accessible chromatin sequencing (ATAC-seq) and enzymatic methyl sequencing.

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ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome

Project description:DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the highly ordered steps of gene regulation. An analysis of independent datasets show an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady state stem cells, suggesting that two opposing features might exist concurrently. To temporally define the relationship between these two events, we developed ATAC-Me, which probes accessibility and methylation from a single library preparation. We identified waves of accessibility, both transient and persistent, occurring rapidly across thousands of myeloid enhancers as monocyte cells transition to a macrophage state. Persistent methylation states were observed at a majority of these sites while transcriptional responses of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation.

2019-05-01 | GSE130096 | GEO

ATAC-seq of Chamaelirium luteum to determine the accessible chromatin regions

Project description:To determine the accessible chromatin regions of Chamaelirium luteum genome, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to generate the genome-wide chromatin accessibility profile.

2025-11-13 | GSE285102 | GEO

ATAC-seq of mouse embryonic stem cells

Project description:To identify the accessible chromatin in wild-type mouse embryonic stem cells (mESCs), we performed ATAC-seq in mESCs.

2021-01-05 | E-MTAB-9245 | biostudies-arrayexpress

Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin with biotinylated transposons [ATAC-seq]

Project description:This study introduced a method for directly identifying the transcriptional machinery on accessible chromatin (ATAC-MS) in a proteome scale. The goals of this study are to integrate ATAC-seq with ATAC-MS to investigate the real-time in vivo transcriptional regulatory processes in organisms.

2024-01-16 | GSE180398 | GEO

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