MSL2 ensures biallelic gene expression in mammals.

In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear.

Identification of regulatory links between transcription and RNA processing with long-read sequencing.

We present a detailed protocol for sequencing full-length mRNA isoforms using the Oxford nanopore long-read sequencing technology. We describe steps for poly(A) RNA isolation, library preparation, and cDNA size selection. We then detail procedures for sequencing and processing and a computational framework to identify exon couplings and assign mRNA 5' ends and 3' ends to each other.

Sites of transcription initiation drive mRNA isoform selection.

The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Here, we assess the regulatory relationships between transcription initiation, alternative splicing, and 3' end site selection. Applying long-read sequencing to accurately represent even the longest transcripts from end to end, we quantify mRNA isoforms in Drosophila tissues, including the transcriptionally complex nervous system.

A Webinar to Improve Parental COVID-19 Vaccine Hesitancy.

Introduction: COVID-19 is a deadly worldwide pandemic and has led to rapid vaccine development. Vaccinating children is a key step to ending the pandemic.

Method: This project used a pretest-posttest design to determine if a 1-hr webinar improved parental COVID-19 vaccine hesitancy.

Isolation and Processing of Murine White Adipocytes for Transcriptome and Epigenome Analyses.

Obesity is a complex disease influenced by genetics, epigenetics, the environment, and their interactions. Mature adipocytes represent the major cell type in white adipose tissue. Understanding how adipocytes function and respond to (epi)genetic and environmental signals is essential for identifying the cause(s) of obesity.

Prognostic impact of the updated 2018 HFA-ESC definition of advanced heart failure: results from the HELP-HF registry.

Aims: The Heart Failure Association of the European Society of Cardiology (HFA-ESC) proposed a definition of advanced heart failure (HF) that has not been validated, yet. We assessed its prognostic impact in a consecutive series of patients with high-risk HF.

Methods And Results: The HELP-HF registry enrolled consecutive patients with HF and at least one high-risk 'I NEED HELP' marker, evaluated at four Italian centres between 1 January 2020 and 30 November 2021.

The glucose transporter GLUT3 controls T helper 17 cell responses through glycolytic-epigenetic reprogramming.

Metabolic reprogramming is a hallmark of activated T cells. The switch from oxidative phosphorylation to aerobic glycolysis provides energy and intermediary metabolites for the biosynthesis of macromolecules to support clonal expansion and effector function. Here, we show that glycolytic reprogramming additionally controls inflammatory gene expression via epigenetic remodeling.

Leadless pacemaker: State of the art and incoming developments to broaden indications.

Theleadless pacemaker (LLPM) therapy has been developed in recent years to overcome the transvenous lead and device pocket-related complications. The LLPMs now available are self-contained right ventricular pacemakers and are limited to single-chamber ventricular pacing modality. This literature review deals with the current status of LLPM technology and current areas of clinical applicability.

DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility.

During neuronal differentiation, the transcriptional profile and the epigenetic context of neural committed cells is subject to significant rearrangements, but a systematic quantification of global histone modification changes is still missing. Here, we show that H3K79me2 increases and H3K27ac decreases globally during in-vitro neuronal differentiation of murine embryonic stem cells. DOT1L mediates all three degrees of methylation of H3K79 and its enzymatic activity is critical to modulate cellular differentiation and reprogramming.

AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis.

CRUP: a comprehensive framework to predict condition-specific regulatory units.

We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes.

Cardiac conduction defects.

Defects in cardiac electric impulse formation or conduction can lead to an irregular beat (arrhythmia) that can cause sudden death without any apparent cause or after stress. In the following sections, we describe the genetic disorders associated with primary cardiac conduction defects, primarily caused by mutations in ion channel genes. Primary indicates that these disorders are not caused by drugs and are not secondary to other disorders like cardiomyopathies (described in the next section).

Real-world 2-year outcome of atrial fibrillation treatment with dabigatran, apixaban, and rivaroxaban in patients with and without chronic kidney disease.

Patients with non-valvular atrial fibrillation (NVAF) and chronic kidney disease (CKD) are at increased risk of stroke and bleeding. Although direct oral anticoagulant (DOAC) trials excluded patients with severe CKD, a growing portion of CKD patients have been starting DOACs and limited data from real-world outcome in this high-risk setting are available. The INSigHT registry included 632 consecutive NVAF patients that started apixaban (256 patients, 41%), dabigatran (245, 39%) and rivaroxaban (131, 20%) between 2012 and 2015.

RELACS nuclei barcoding enables high-throughput ChIP-seq.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques.

Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations.

Pluripotent stem cells are invaluable resources to study development and disease, holding a great promise for regenerative medicine. Here we use human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) from patients with Huntington's disease (HD-iPSCs) to shed light into the normal function of huntingtin (HTT) and its demise in disease. We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1.

A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.

Background: Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them.

Parkour LIMS: high-quality sample preparation in next generation sequencing.

Motivation: This paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples.

Results: Starting with user requests, Parkour allows tracking and assessing samples based on predefined quality criteria through different stages of the sample preparation workflow. Ideally suited for academic core laboratories, the software aims to maximize efficiency and reduce turnaround time by intelligent sample grouping and a clear assignment of staff to work units.

Two-year cardiac mortality after MitraClip treatment of functional mitral regurgitation in ischemic and non-ischemic dilated cardiomyopathy.

Background: MitraClip implantation has evolved as a new tool for treatment of inoperable or high-risk patients with severe functional mitral regurgitation (FMR) due to dilated cardiomyopathy (DCM). Limited data are available regarding MitraClip outcomes comparing patients with ischemic and non-ischemic DCM.

Methods: From 2008 to 2016, 314 patients received MitraClip for FMR at four institutions: Brescia, Zurich and Milan.

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes.

To date, it remains largely unclear to what extent chromatin machinery contributes to the susceptibility and progression of complex diseases. Here, we combine deep epigenome mapping with single-cell transcriptomics to mine for evidence of chromatin dysregulation in type 2 diabetes. We find two chromatin-state signatures that track β cell dysfunction in mice and humans: ectopic activation of bivalent Polycomb-silenced domains and loss of expression at an epigenomically unique class of lineage-defining genes.

High-resolution TADs reveal DNA sequences underlying genome organization in flies.

Despite an abundance of new studies about topologically associating domains (TADs), the role of genetic information in TAD formation is still not fully understood. Here we use our software, HiCExplorer (hicexplorer.readthedocs.

The histone code reader Spin1 controls skeletal muscle development.

While several studies correlated increased expression of the histone code reader Spin1 with tumor formation or growth, little is known about physiological functions of the protein. We generated Spin1 mice with ablation of Spin1 in myoblast precursors using the Myf5-Cre deleter strain. Most Spin1 mice die shortly after birth displaying severe sarcomere disorganization and necrosis.

Polymer-free amphilimus-eluting stent versus biodegradable polymer biolimus-eluting stent in patients with and without diabetes mellitus.

Objectives: This study sought to compare clinical outcome of polymer-free amphilimus-eluting stent (PF-AES) versus biodegradable-polymer biolimus-eluting stent (BD-BES) in "all-comer" diabetes mellitus (DM) and non-DM patients who underwent percutaneous coronary intervention.

Background: The PF-AES has shown promising preliminary results in patients with DM.

Methods: Data from 2 multicentre-national registries (the ASTUTE and the INSPIRE-1) were used to analyse 1776 patients stratified in non-DM and DM.

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4.

Coordination of energy metabolism is essential for homeostasis of stem cells, whereas an imbalance in energy homeostasis causes disease and accelerated aging. Here we show that deletion or enzymatic inactivation of lysine-specific demethylase 1 (Lsd1) triggers senescence in trophoblast stem cells (TSCs). Genome-wide transcriptional profiling of TSCs following Lsd1 inhibition shows gene set enrichment of aging and metabolic pathways.