Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure

Informationen des Genoms werden nicht nur mit der Sequenz oder epigenetischen Modifikation codiert, sondern auch in ihrer Faltung im 3D-Raum gefunden. Jüngste Entwicklungen bei der Konformationserfassung von Chromosomen ermöglichten es uns, die räumliche Positionierung des Genoms in verschiedenen Maßstäben aufzudecken. Die Bildung selbstinteragierender Genomregionen, die als Topologically Associated Domains (TADs) bezeichnet werden, wird von Hi-C als Schlüsselmerkmal der Genomorganisation jenseits der Nukleosomenebene entdeckt. Jedes TAD ist eine isolierte lokale Packungseinheit, in der Intra-TADWechselwirkungen bevorzugt und Inter-TAD-Wechselwirkungen isoliert werden. Bei Tieren wird gezeigt, dass mehrere Architekturproteine zur Struktur und Funktion der tierischen TADs beitragen. Im Gegensatz zu Tieren sind TAD-Bildung, - Funktion und -Proteine, die bei diesen Prozessen in Pflanzen eine Rolle spielen, eher unbekannt. Unsere vorläufige Hi-C-Analyse zeigte, dass das Genom von Marchantia polymorpha, einem Mitglied einer basalen Landpflanzenlinie, eine evolutionär konservierte 3DLandschaft mit dem höheren Pflanzen teilt. Das Marchantia-Genom ist in Hunderte von TADs unterteilt und ihre Grenzen sind mit der TCP1-Proteinbindung verbunden. Eine genomweite epigenetische Analyse ergab, dass ein beträchtlicher Teil der Marchantia-TADs interstitielles Heterochromatin darstellt und mit repressiven epigenetischen Markierungen verziert ist. Wir identifizieren auch einen neuartigen TAD-Typ, den wir TCP1-reiches TAD nennen, bei dem genomische Regionen gut zugänglich und durch TCP1-Proteine dicht gebunden sind. TCP1- gebundene Gene, die sich in TCP1-reichen TADs befinden, weisen im Vergleich zu TCP1-gebundenen Genen an anderen Stellen niedrigere Genexpressionsniveaus auf. In tcp1-Mutanten änderten sich die TAD-Muster in der Hi-C-Karte nicht, was darauf hinweist, dass das TCP1-Protein für die TAD-Bildung und -Struktur nicht wesentlich ist. Wir stellen jedoch fest, dass in tcp1-Mutanten Gene, die in TCP1-reichen TADs leben, eine größere Veränderung der Expressionsfalte aufweisen als Gene, die nicht zu diesen TADs gehören. Unsere Ergebnisse zeigen, dass Pflanzen-TADs nicht nur als räumliche Chromatin-Packungsmodule stehen, sondern auch als nukleare Mikrokompartimente fungieren, die die Aktivitäten des Transkriptionsfaktors korrelieren.Information of the genome is not only encoded to its sequence or epigenetic modifications but also found in its folding in 3D space. Recent developments in Chromosome Conformation Capture techniques enabled us to unveil spatial positioning of the genome at different scales. The formation of self-interacting genomic regions, named Topologically Associated Domains (TADs), are discovered by Hi-C, as a key feature of genome organization beyond the nucleosomal level. Each TAD is an isolated local packing unit in which intra-TAD interactions are favoured and inter-TAD interactions are insulated. In animals several architectural proteins are shown to contribute the structure and the function of the animal TADs. Unlike those in animals, TAD formation, function and proteins that play a role in these processes in plants are rather unknown. Our Hi-C analyses show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, shares an evolutionary conserved 3D landscape with that of higher plants. The Marchantia genome is subdivided into hundreds of TADs and their borders are associated with TCP1 protein binding. Genome-wide epigenetic analysis reveals that a considerable fraction of Marchantia TADs represent interstitial heterochromatin and are decorated with repressive epigenetic marks. We also identify a novel type of TAD that we name TCP1-rich TAD, in which genomic regions are highly accessible and densely bound by TCP1 proteins. TCP1-bound genes residing in TCP1-rich TADs exhibit lower gene expression levels compared to the TCP1- bound genes in other locations. In tcp1 mutants, TAD patterns in the Hi-C map do not change, indicating that TCP1 protein is not essential for TAD formation and structure. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent in expression fold change compared to genes not belonging to these TADs. Our results indicate that, besides standing as spatial chromatin packing modules, plant TADs function as nuclear micro-compartments that correlate transcription factor activities

Cytokine Profiles of Chronic Urticaria Patients and the Effects of Omalizumab Treatment

Introduction: Cytokines are key mediators in immunological and inflammatory conditions, including chronic spontaneous urticaria (CSU). Objectives: To investigate Th1, Th2, and Th17 cytokine profiles in CSU and to evaluate the possible effect of omalizumab treatment. Methods: Patients who were followed up for CSU, as well as healthy volunteers, were included in the study. To assess urticaria activity, the 7-day-Urticaria Activity Score (UAS-7), the Urticaria Control Test (UCT), and the Chronic Urticaria Quality of Life Questionnaire (CU-QoL) were filled. Serum levels of IL-6, IL-17, IL-31, eotaxin, RANTES, TNF-α, and TSLP were analyzed by ELISA and compared in CSU and control groups. The patients were analyzed in two groups as the omalizumab group and the non-omalizumab group based on their treatment status.   Results: Total IgE, ESR, CRP, RANTES, and TNF-a were significantly different in the overall comparison of the three groups: CSU-receiving omalizumab, CSU-not receiving omalizumab, and control groups (P <0.01, 0.015, <0.01, <0.01 and <0.01 respectively). Total IgE, CRP, RANTES, and TNF-α values were similar in those who received and did not receive omalizumab, yet these biomarkers were significantly higher in both groups than in the control group (P < 0.05). Statistical significance in ESR was observed only between the CSU-receiving omalizumab group and the control group (P = 0.01). Within the CSU patients, there was a slight but significant correlation between UCT and TNF-α (P = 0.008, r = 0.32) and IL-17 (P = 0.06, r = 0.33) levels. Conclusions: The investigated cytokine profile in CSU patients may differ from healthy controls, particularly with the higher levels of RANTES and TNF-α, and omalizumab treatment does not seem to affect that profile in CSU patients

Omics technologies in allergy and asthma research: An EAACI position paper

Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force “Omics technologies in allergic research” broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients’ stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted

Three-dimensional chromatin packing and positioning of plant genomes

Review article

Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes

The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response