Genome-wide epigenetic profiling and transcriptome analysis in pediatric Obstructive Sleep Apnea: A focus on Black female children.

Obstructive Sleep Apnea (OSA) is a common sleep-related breathing disorder characterized by airway obstruction during sleep. Diagnosing pediatric OSA is challenging, particularly in underrepresented populations, leading to disparities in treatment and long-term negative health outcomes. Our study aimed to identify alternative diagnostic tools by investigating genome-wide epigenetic changes and associated transcriptomic alterations in Black female, pediatric patients with OSA.

Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity.

Human cytomegalovirus (HCMV) infects up to 80% of the world's population. Here, we show that HCMV infection leads to widespread changes in human chromatin accessibility and chromatin looping, with hundreds of thousands of genomic regions affected 48 hours after infection. Integrative analyses reveal HCMV-induced perturbation of Hippo signaling through drastic reduction of TEAD1 transcription factor activity.

Macrophage memories of early-life injury drive neonatal nociceptive priming.

The developing peripheral nervous and immune systems are functionally distinct from those of adults. These systems are vulnerable to early-life injury, which influences outcomes related to nociception following subsequent injury later in life (i.e.

Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome.

Background: There are two major genetic types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein-Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) such as RBPJ, EBF1, and SPI1 (PU.

Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis.

Eosinophilic esophagitis (EoE) is a rare atopic disorder associated with esophageal dysfunction, including difficulty swallowing, food impaction, and inflammation, that develops in a small subset of people with food allergies. Genome-wide association studies (GWASs) have identified 9 independent EoE risk loci reaching genome-wide significance (p < 5 × 10) and 27 additional loci of suggestive significance (5 × 10 < p < 1 × 10). In the current study, we perform linkage disequilibrium (LD) expansion of these loci to nominate a set of 531 variants that are potentially causal.

Effector memory T cells induce innate inflammation by triggering DNA damage and a non-canonical STING pathway in dendritic cells.

Cognate interaction between CD4 effector memory T (T) cells and dendritic cells (DCs) induces innate inflammatory cytokine production, resulting in detrimental autoimmune pathology and cytokine storms. While T cells use tumor necrosis factor (TNF) superfamily ligands to activate DCs, whether T cells prompt other DC-intrinsic changes that influence the innate inflammatory response has never been investigated. We report the surprising discovery that T cells trigger double-strand DNA breaks via mitochondrial reactive oxygen species (ROS) production in interacting DCs.

Macrophage epigenetic memories of early life injury drive neonatal nociceptive priming.

The developing peripheral nervous and immune systems are functionally distinct from adults. These systems are vulnerable to early life injury, which influences outcomes related to nociception following subsequent injury later in life (neonatal nociceptive priming). The underpinnings of this phenomenon are largely unknown, although previous work indicates that macrophages are epigenetically trained by inflammation and injury.

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods for TFBS prediction from DNase-seq.

Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis.

Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells.

Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci.

The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we showed that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders.

Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets.

Runt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion of Runx1 in mouse metanephric mesenchyme-derived mK4 cells results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci enriched for Runx sites in mK4 cells lose chromatin accessibility in Runx1 knockout cells, despite remaining Runx2-bound.

Global discovery of lupus genetic risk variant allelic enhancer activity.

Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci.

Effects of Thermal Annealing and Selective Chemical Etching on Structural and Optical Properties of GaAsBi Epilayer with Droplet Systems.

A GaAsBi layer was grown by molecular beam epitaxy (MBE) with a low Bi content (2.3%) on GaAs maintaining the substrate at a non-rotating state and was then annealed at 750 °C, 800 °C and 850 °C. Each sample that was covered with droplets was investigated by using the Atomic Force Microscopy (AFM), Electrostatic Force Microscopy (EFM) and Photoluminescence (PL) techniques.

Magnetotransport study on as-grown and annealed n- and p-type modulation-doped GaInNAs/GaAs strained quantum well structures.

Unlabelled: We report the observation of thermal annealing- and nitrogen-induced effects on electronic transport properties of as-grown and annealed n- and p-type modulation-doped Ga1 - xInxNyAs1 - y (x = 0.32, y = 0, 0.009, and 0.

Bismuth-induced effects on optical, lattice vibrational, and structural properties of bulk GaAsBi alloys.

Unlabelled: Bulk GaAs1 - xBix/GaAs alloys with various bismuth compositions are studied using power- and temperature-dependent photoluminescence (PL), Raman scattering, and atomic force microscopy (AFM). PL measurements exhibit that the bandgap of the alloy decreases with increasing bismuth composition. Moreover, PL peak energy and PL characteristic are found to be excitation intensity dependent.

Excitation energy-dependent nature of Raman scattering spectrum in GaInNAs/GaAs quantum well structures.

The excitation energy-dependent nature of Raman scattering spectrum, vibration, electronic or both, has been studied using different excitation sources on as-grown and annealed n- and p-type modulation-doped Ga1 - xInxNyAs1 - y/GaAs quantum well structures. The samples were grown by molecular beam technique with different N concentrations (y = 0%, 0.9%, 1.

A study of photomodulated reflectance on staircase-like, n-doped GaAs/AlxGa1-xAs quantum well structures.

In this study, photomodulated reflectance (PR) technique was employed on two different quantum well infrared photodetector (QWIP) structures, which consist of n-doped GaAs quantum wells (QWs) between undoped AlxGa1-xAs barriers with three different x compositions. Therefore, the barrier profile is in the form of a staircase-like barrier. The main difference between the two structures is the doping profile and the doping concentration of the QWs.

An analysis of Hall mobility in as-grown and annealed n- and p-type modulation-doped GaInNAs/GaAs quantum wells.

In this study, we investigate the effect of annealing and nitrogen amount on electronic transport properties in n- and p-type-doped Ga0.68In0.32NyAs1 - y/GaAs quantum well (QW) structures with y = 0%, 0.

The role of dislocation-induced scattering in electronic transport in GaxIn1-xN alloys.

Electronic transport in unintentionally doped GaxIn1-xN alloys with various Ga concentrations (x = 0.06, 0.32 and 0.