3D ATAC-PALM: super-resolution imaging of the accessible genome.

08:00 EDT 16th March 2020 | BioPortfolio

Summary of "3D ATAC-PALM: super-resolution imaging of the accessible genome."

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.


Journal Details

This article was published in the following journal.

Name: Nature methods
ISSN: 1548-7105


DeepDyve research library

PubMed Articles [13088 Associated PubMed Articles listed on BioPortfolio]

Label-free STORM principle realized by super-Rayleigh speckle in photoacoustic imaging.

Photoacoustic (PA) imaging can provide information hidden deep inside biological tissues; however, its resolution is limited by acoustic diffraction. It has been demonstrated that the uncontrolled spe...

Super-Beacons: Open-Source Probes With Spontaneous Tuneable Blinking Compatible With Live-Cell Super-Resolution Microscopy.

Localization based super-resolution microscopy relies on the detection of individual molecules cycling between fluorescent and non-fluorescent states. These transitions are commonly regulated by high-...

High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT.

Super-resolution imaging allows for visualization of cellular structures on a nanoscale level. DNA-PAINT (DNA Point Accumulation In Nanoscale Topology) is a super-resolution method that depends on the...

Multiscale brain MRI super-resolution using deep 3D convolutional networks.

The purpose of super-resolution approaches is to overcome the hardware limitations and the clinical requirements of imaging procedures by reconstructing high-resolution images from low-resolution acqu...

Super-resolution of cardiac magnetic resonance images using Laplacian Pyramid based on Generative Adversarial Networks.

Cardiac magnetic resonance imaging (MRI) can assist in both functional and structural analysis of the heart, but due to hardware and physical limitations, high-resolution MRI scans is time consuming a...

Clinical Trials [5685 Associated Clinical Trials listed on BioPortfolio]

Neuroprotective and Cardioprotective Effects Of Palm Vitamin E Tocotrienols

The purpose of the study is to assess the neuroprotective, anti atherogenic and hepatoprotective properties of tocotrienols (palm vitamin E) supplementation as determined by white matter l...

Modulating Effects of Oil Palm Phenolics in Subjects With Pre-diabetes

Study reported that providing Oil Palm Phenolics to Nile rats blocked diabetes progression in this spontaneous diabetes model. The present study aims to determine the beneficial effects of...

Multimodal Ophthalmic Imaging

Knowledge of the pathogenesis of ocular conditions, a leading cause of blindness, has benefited greatly from recent advances in ophthalmic imaging. However, current clinical imaging system...

Evaluation of the Effect of Palm Olein Free Formula on Intestinal Flora and Gastrointestinal Tolerance

Depending on recent studies in literature the investigators aimed to compare whether gastrointestinal tolerance differs between infants fed with palm olein containing or palm olein free fo...

Magnetic Resonance Imaging (MRI) for Aortic Dissection to Visualise Inflammation

The study is a single-centre, prospective, observational cross-sectional imaging study aimed to determine if macrophage-mediated inflammation can be visualised in the aorta of patients wit...

Medical and Biotech [MESH] Definitions

High resolution imaging techniques that allow visualization of individual molecules of proteins, lipids, or nucleic acids within cells or tissues.

Magnetic resonance imaging diagnostic technique which uses fluorine-19 perfluorocarbon probes and contrast agents for high resolution image detection and quantitation.

The use of molecularly targeted imaging probes to localize and/or monitor biochemical and cellular processes via various imaging modalities that include RADIONUCLIDE IMAGING; ULTRASONOGRAPHY; MAGNETIC RESONANCE IMAGING; fluorescence imaging; and MICROSCOPY.

Nutritive oil extracted from the fleshy mesocarp of the fruit of the African palm tree, Elaeis guineensis.

Nanometer-sized tubes composed mainly of CARBON. Such nanotubes are used as probes for high-resolution structural and chemical imaging of biomolecules with ATOMIC FORCE MICROSCOPY.

Quick Search

DeepDyve research library

Relevant Topics

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

An assay is an analytic procedure for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity.  This can be a drug or biochemical substance or a cell in an organism or organic sample. ...

Searches Linking to this Article