ATAC see

Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways...

BACKGROUND: Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values...

Assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that enables direct imaging of the accessible genome in situ and deep sequencing to reveal the identity of the imaged elements. Here we image spatial organization of the accessible genome in HT1080 cells with this method.

Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.

In this issue of Cancer Discovery, Penter and colleagues describe the results of applying the recently described technology of combined assay for transposase-accessible chromatin using sequencing and mitochondrial DNA sequencing in single cells from serial samples from nine patients with chronic lymphocytic leukemia. The naturally occurring barcodes, provided by mitochondrial DNA mutations, allowed tracking of subclones with distinct chromatin accessibility profiles and copy-number alterations demonstrating distinct patterns of tumor evolution under a range of selection pressures...

Moiré superlattices in transition metal dichalcogenide bilayers provide a platform for exploring strong correlations with optical spectroscopy. Despite the observation of rich Mott-Wigner physics stemming from an interplay between the periodic potential and Coulomb interactions, the absence of tunnel coupling–induced hybridization of electronic states has ensured a classical layer degree of freedom. We investigated a MoSe2 homobilayer structure where interlayer coherent tunneling allows for electric field–controlled manipulation and measurement of the ground-state hole-layer pseudospin...

Neural crest stem/progenitor cells arise early during vertebrate embryogenesis at the border of the forming central nervous system. They subsequently migrate throughout the body, eventually differentiating into diverse cell types ranging from neurons and glia of the peripheral nervous system to bones of the face, portions of the heart, and pigmentation of the skin. Along the body axis, the neural crest is heterogeneous, with different subpopulations arising in the head, neck, trunk, and tail regions, each characterized by distinct migratory patterns and developmental potential...

The neutron is a cornerstone in our depiction of the visible universe. Despite the neutron zero-net electric charge, the asymmetric distribution of the positively- (up) and negatively-charged (down) quarks, a result of the complex quark-gluon dynamics, lead to a negative value for its squared charge radius, [Formula: see text]. The precise measurement of the neutron's charge radius thus emerges as an essential part of unraveling its structure. Here we report on a [Formula: see text] measurement, based on the extraction of the neutron electric form factor, [Formula: see text], at low four-momentum transfer squared (Q2 ) by exploiting the long known connection between the N → Δ quadrupole transitions and the neutron electric form factor...

Splicing of precursor messenger RNA is catalyzed by the spliceosome, a dynamic ribonucleoprotein assembly including five small nuclear (sn)RNAs and >100 proteins. RNA components catalyze the two transesterification reactions, but proteins perform critical roles in assembly and rearrangement. The catalytic core comprises a paired complex of U2 and U6 snRNAs for the major form of the spliceosome and U12 and U6atac snRNAs for the minor variant (∼0.3% of all spliceosomes in higher eukaryotes); the latter shares key catalytic sequence elements and performs identical chemistry...

Chromatin accessibility is a predictor of gene expression, cell division, and cell type specificity. NicE-viewSeq (Nicking Enzyme-assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S, and G2/M)-specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations...

We construct a simple workflow for fluent genomics data analysis using the R/Bioconductor ecosystem. This involves three core steps: import  the data into an appropriate abstraction, model the data with respect to the biological questions of interest, and integrate the results with respect to their underlying genomic coordinates. Here we show how to implement these steps to integrate published RNA-seq and ATAC-seq experiments on macrophage cell lines. Using tximeta , we import  RNA-seq transcript quantifications into an analysis-ready data structure, called the SummarizedExperiment , that contains the ranges of the reference transcripts and metadata on their provenance...

BACKGROUND: Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein lamin A (termed progerin) and have previously been shown to exhibit prominent histone modification changes. METHODS: Here, we analyze the possibility that epigenetic deregulation of lamina-associated domains (LADs) is involved in the molecular pathology of HGPS...

Lysine acetyltransferase 6A (KAT6A) and its paralog KAT6B form stoichiometric complexes with bromodomain- and PHD finger-containing protein 1 (BRPF1) for acetylation of histone H3 at lysine 23 (H3K23). We report that these complexes also catalyze H3K23 propionylation in vitro and in vivo. Immunofluorescence microscopy and ATAC-See revealed the association of this modification with active chromatin. Brpf1 deletion obliterates the acylation in mouse embryos and fibroblasts. Moreover, we identify BRPF1 variants in 12 previously unidentified cases of syndromic intellectual disability and demonstrate that these cases and known BRPF1 variants impair H3K23 propionylation...

The transcription factor c-Myb is involved in early differentiation and proliferation of haematopoietic cells, where it operates as a regulator of self-renewal and multi-lineage differentiation. Deregulated c-Myb plays critical roles in leukaemias and other human cancers. Due to its role as a master regulator, we hypothesized it might function as a pioneer transcription factor. Our approach to test this was to analyse a mutant of c-Myb, D152V, previously reported to cause haematopoietic defects in mice by an unknown mechanism...

Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis...

This study aimed to examine the thoughts and expectations of patients receiving healthcare from their physicians and evaluate the ethical aspects of these thoughts and expectations. To determine the ethical aspects of the thoughts and expectations of patients, an open-ended question was asked on the web page of the Turkish Armed Forces (TAF) Health Care Command, which is accessible to the users of the TAF intranet system (the internet system used within TAF institutions). The participants were asked to express their thoughts in their own words...

BACKGROUND: When the mechanism of action behind treatment toxicity reflects the intended effect on the treatment target, the toxicity might be a useful marker for efficacy. During endocrine treatment of breast cancer, the occurrence of symptoms related to oestrogen depletion or oestrogen blockade might thus be a predictor of treatment effectiveness. In this retrospective analysis, the relation between the reported incidence of vasomotor or joint symptoms and breast cancer recurrence in the Arimidex, Tamoxifen, Alone or in Combination (ATAC) trial is assessed...

In order to define the precise locations of precentral and postcentral gyri during neurosurgical operations, somatosensory evoked potentials to contralateral median nerve stimulation were recorded from the cerebral cortex in 19 cases with organic cerebral lesions which located near the central sulcus. In addition to that, distribution patterns of early components of SEPs were displayed by Nihonkoden Atac 450 in 3 cases who had bone defects after wide decompressive craniectomy but were without any sensory disturbances In 4 cases, in whom deep electrodes were inserted for the stereotaxic operations or other reasons, frontal subcortical SEPs were recorded in order to know the origins of frontal components of SEPs...