ATAC-Seq to investigate the spatial choreography of the accessible genome
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE79921 | GEO | 2016/10/13
SECONDARY ACCESSION(S): PRJNA317466
REPOSITORIES: GEO
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Project description:In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression.
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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.
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Project description:we combined Assay for Transposase-Accessible Chromatin and lattice light-sheet PALM microscopy (3D ATAC-PALM) to selectively image key features of the 3D accessible genome in single cells. We found that accessible chromatin domains (ACDs) form spatially segregated clusters in the nucleus. Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced extensive 3D spatial mixing of ACD clusters and reduced physical separation between ACDs within chromosomes. Experimental perturbations and modeling suggest that both weak, multivalent, dynamic protein-protein interactions together with loop extrusion influence ACD organization. Live-cell studies suggest that ACD clustering regulates transcription factor binding site distribution, target search kinetics and binding dynamics. Here we report the ATAC-seq results from Tn5 PA549 and nextera Tn5 upon various chemical and genetic perturbations.
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