Epigenomics and Chromatin Dynamics

A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest Keystone meetings to date, reflecting the excitement and many developments in this area. Richard Young opened the meeting by giving a historic overview before sharing more detailed insights from his recent work in describing the role of the lysine demethylase Lsd1 in mouse embryonic stem (ES) cell differentiation. He also set the broader stage and highlighted the excitement concerning recent advances in epigenetic drugs such as the new bromodomain inhibitors.Stem Cell and Regenerative Biolog

Ueber die Wasserstoffionenkonzentration an den Sekreten und Schleimhauten bei Nasen-Kieferhohlen- und Rachenerkrankungen

Auf dem Oto-Rhino-und Laryngologischen Gebiet sind bisher physikalisch-chemische Untersuchungen sehr wenig erforscht worden, besonders liegen hier nur sparliche Studien uber das Verhalten der Wasserstoffionenkonzentration vor. Ich habe mit Hilfe der Chinhydronelektrode das PH in den Sekreten bei Rhinitis chronica, Sinuitis maxillaris chronica gemessen, sowie an den Hohlenschleimhauten bei Sinuitis maxillaris chronica, gleichfalls in den Gewebssaften bei Gaumen- und Rachen-tonsillitiden bestimmt. Aus den erhaltenen PH-Werten in Zusammenhang mit dem Krankheitsverlauf lassen sich folgende Schlusse ziehen: 1. PH-Werte: In Nasensekreten bei Rhinitis Katarrhalis chronica 7.68-8.10, wahrend als normales PH bei Gesunden 8.10-8.33 festgestellt wurde. An den Krusten bei Rhinitis atrophicans chronica betrug das PH 6.79-7.35, dagegen an den unterhalb der Krusten sich befindlichen weichen Sekreten PH 7.52-8.0.2. 2. Die Staungssekrete bei Sinuitis maxillaris chronica zeigten ein PH 6.19-8.09. In rein eitrigen Sekreten bei eitriger Form der Erkrankung fand eine Verschiebung nach der sauren, in den schleimigen bei katarrhalischer Form nach der alkalischen Seite hin statt, und bei den ersteren befanden sich die Eiterzellen in hochgradigen Regressionszu-standen, welche Prozesse bei den letzteren verhaltnissmassig geringfugig waren. An den klar gelblichen, flussigen Sekreten bei Zysten und Hydrops bekam man PH=7.39-7.45, ein Alkalitatsgrad, welcher dem PH des Blutes bei normalen Menschen entspricht. Es ist also anzunehmen, dass der PH-Wert der Sekrete das Ergebnis der Mischung der einzelnen Komponenten der Absonderung (Eiter, Schleim, Exsudat) ist und gleichzeitig von der Starke der regressiven Degeneration der Eiterzellen abhangt. 3. Mit der Erleichterung der Symptome durch geeignete Hohlenspulung bei Sinuitis maxillaris chronica gehen die regressiven Prozesse an den Eiterzellen auch zuruck, steigen die PH-Werte bis etwas 8.0 an, dann pflegt das Leiden allmahich zur Heilung zu kommen. Die PH-Betrage und die Starke der regressive

The Role of Cell-polarity in Development and Disease

From the simplest unicellular organisms to complex metazoans, cell polarity is a widespread characteristic that is essential for almost every aspect of biology. Proper polarization of cells is crucial for the establishment and maintenance of higher order structures such as tissue and organs. Cell polarity refers to the asymmetric distribution of various macromolecules and cellular structures, resulting in polarized architecture and function of the cell. Defects in cell polarity lead to various phenotypes, ranging from aberrant signaling, proliferation, cell adhesion and migration, cell fate determination and pluripotency, as well as embryonic lethality, neoplasia and cancer. Given the various roles for cell polarity in development and disease, the characterization of the components involved in polarity and their mechanisms of function is of great importance. My thesis work has encompassed three major projects, each of which is focused on understanding the role of cell polarity in development and disease. Although genetic screens in invertebrates have led to the identification of a number of cell-polarity proteins, similar systematic approach have not been undertaken in mammalian systems. The goal of my first project was to design and implement a high-throughput screen to systematically knockdown individual genes using siRNA, and then assess cell junction integrity as a measure of cell polarity. Given the importance of cell polarity to signaling pathways, I next sought to determine the mechanism by which cell polarity affects TGFβ and Hippo pathways, two important signaling pathways involved in development and disease. Lastly, by studying the acquisition of pluripotency by somatic cells, I uncovered a central role for cell polarity in the establishment and maintenance of pluripotency. Here I will present and discuss our discovery pertaining to the role of cell polarity in cell signaling and pluripotency.Ph

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

Abstract Background Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genome biology of TOP2B, we used proteomics (BioID), chromatin immunoprecipitation, and high-throughput chromosome conformation capture (Hi-C) to identify novel proximal TOP2B protein interactions and characterize the genomic landscape of TOP2B binding at base pair resolution. Results Our human TOP2B proximal protein interaction network included members of the cohesin complex and nucleolar proteins associated with rDNA biology. TOP2B associates with DNase I hypersensitivity sites, allele-specific transcription factor (TF) binding, and evolutionarily conserved TF binding sites on the mouse genome. Approximately half of all CTCF/cohesion-bound regions coincided with TOP2B binding. Base pair resolution ChIP-exo mapping of TOP2B, CTCF, and cohesin sites revealed a striking structural ordering of these proteins along the genome relative to the CTCF motif. These ordered TOP2B-CTCF-cohesin sites flank the boundaries of topologically associating domains (TADs) with TOP2B positioned externally and cohesin internally to the domain loop. Conclusions TOP2B is positioned to solve topological problems at diverse cis-regulatory elements and its occupancy is a highly ordered and prevalent feature of CTCF/cohesin binding sites that flank TADs

Preparation of iPSCs for Targeted Proteomic Analysis

Induced pluripotent stem cells have great potential as a human model system in regenerative medicine, disease modelling and drug screening. However, extensive analysis of iPSC are required before their therapeutic applications. With recent developments in mass spectrometry and proteomics, this technique can become a great alternative to traditional genomic approaches for iPSC analysis. Here, we describe preparation of iPSC for targeted proteomic analysis, and measurement of pluripotency markers allowing for classification into either pluripotent or non-pluripotent cells

A SARS-CoV-2 – host proximity interactome

Posté sur BioRxiv le 4 septembre 2020 https://www.biorxiv.org/content/10.1101/2020.09.03.282103v1.article-infoViral replication is dependent on interactions between viral polypeptides and host proteins. Identifying virus-host protein interactions can thus uncover unique opportunities for interfering with the virus life cycle via novel drug compounds or drug repurposing. Importantly, many viral-host protein interactions take place at intracellular membranes and poorly soluble organelles, which are difficult to profile using classical biochemical purification approaches. Applying proximity-dependent biotinylation (BioID) with the fast-acting miniTurbo enzyme to 27 SARS-CoV-2 proteins in a lung adenocarcinoma cell line (A549), we detected 7810 proximity interactions (7382 of which are new for SARS-CoV-2) with 2242 host proteins (results available at covid19interactome.org). These results complement and dramatically expand upon recent affinity purification-based studies identifying stable host-virus protein complexes, and offer an unparalleled view of membrane-associated processes critical for viral production. Host cell organellar markers were also subjected to BioID in parallel, allowing us to propose modes of action for several viral proteins in the context of host proteome remodelling. In summary, our dataset identifies numerous high confidence proximity partners for SARS-CoV-2 viral proteins, and describes potential mechanisms for their effects on specific host cell functions

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

International audienc

A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions

International audienceThe world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it