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Schneider C.,ETH Zurich | Nobs S.P.,ETH Zurich | Heer A.K.,ETH Zurich | Hirsch E.,University of Turin | And 3 more authors.
Journal of Leukocyte Biology | Year: 2017

PI3Ks have been identified as key signaling proteins involved in many basic biologic processes in health and disease. Transgenic animals have been essential tools to study the underlying molecular mechanisms in this context and therefore, have been widely used to elucidate the role of these factors in many different settings. More specifically, PI3Kγ, a subunit highly expressed in the hematopoietic system, has been implicated to play an important role in many inflammatory diseases as well as cancer. Here, we report identification of multiple, additional, previously unknown mutations in the genome of a widely used PI3Kγ-deficient (PI3Kγ-/-) mouse colony. These include a STOP mutation in the GM-CSFRα chain, leading to a complete and specific deficiency in GM-CSF signaling. PI3Kγ-/- animals consequently lacked alveolar macrophages (AMs) and succumbed rapidly to influenza virus infection. Furthermore, PI3Kγ-/- mice carried an additional mutation that affects mucin 2 (Muc2) transcripts. This protein is strongly involved in the regulation of colorectal cancer, and indeed, conflicting reports have indicated that PI3Kγ-/- animals spontaneously develop colorectal tumors. Thus, we uncover previously unknown, confounding factors present in a strain of PI3Kγ-/- mice, leading to additional deficiencies in important signaling pathways with potentially wideranging implications for the interpretation of previous studies. By separating the mutations, we established a unique Csf2ra-/- mouse model that allows us to study the role of cell intrinsic GM-CSFR signaling in vivo without confounding variables introduced by defective IL-5R and IL-3R signaling in mice lacking the common b chain (Csf2rb). © Society for Leukocyte Biology.


Lienert F.,Friedrich Miescher Institute for Biomedical Research | Lienert F.,University of Basel | Wirbelauer C.,Friedrich Miescher Institute for Biomedical Research | Som I.,U.S. National Institutes of Health | And 5 more authors.
Nature Genetics | Year: 2011

Cytosine methylation is a repressive, epigenetically propagated DNA modification. Although patterns of DNA methylation seem tightly regulated in mammals, it is unclear how these are specified and to what extent this process entails genetic or epigenetic regulation. To dissect the role of the underlying DNA sequence, we sequentially inserted over 50 different DNA elements into the same genomic locus in mouse stem cells. Promoter sequences of approximately 1,000 bp autonomously recapitulated correct DNA methylation in pluripotent cells. Moreover, they supported proper de novo methylation during differentiation. Truncation analysis revealed that this regulatory potential is contained within small methylation-determining regions (MDRs). MDRs can mediate both hypomethylation and de novo methylation in cis, and their activity depends on developmental state, motifs for DNA-binding factors and a critical CpG density. These results demonstrate that proximal sequence elements are both necessary and sufficient for regulating DNA methylation and reveal basic constraints of this regulation. © 2011 Nature America, Inc. All rights reserved.


Lienert F.,Friedrich Miescher Institute for Biomedical Research | Mohn F.,Friedrich Miescher Institute for Biomedical Research | Mohn F.,Institute of Molecular Biotechnology | Tiwari V.K.,Friedrich Miescher Institute for Biomedical Research | And 5 more authors.
PLoS Genetics | Year: 2011

Cellular differentiation entails reprogramming of the transcriptome from a pluripotent to a unipotent fate. This process was suggested to coincide with a global increase of repressive heterochromatin, which results in a reduction of transcriptional plasticity and potential. Here we report the dynamics of the transcriptome and an abundant heterochromatic histone modification, dimethylation of histone H3 at lysine 9 (H3K9me2), during neuronal differentiation of embryonic stem cells. In contrast to the prevailing model, we find H3K9me2 to occupy over 50% of chromosomal regions already in stem cells. Marked are most genomic regions that are devoid of transcription and a subgroup of histone modifications. Importantly, no global increase occurs during differentiation, but discrete local changes of H3K9me2 particularly at genic regions can be detected. Mirroring the cell fate change, many genes show altered expression upon differentiation. Quantitative sequencing of transcripts demonstrates however that the total number of active genes is equal between stem cells and several tested differentiated cell types. Together, these findings reveal high prevalence of a heterochromatic mark in stem cells and challenge the model of low abundance of epigenetic repression and resulting global basal level transcription in stem cells. This suggests that cellular differentiation entails local rather than global changes in epigenetic repression and transcriptional activity. © 2011 Lienert et al.


Bulut-Karslioglu A.,Max Planck Institute of Immunobiology and Epigenetics | Perrera V.,Max Planck Institute of Immunobiology and Epigenetics | Perrera V.,Research Institute of Molecular Pathology | Scaranaro M.,Research Institute of Molecular Pathology | And 15 more authors.
Nature Structural and Molecular Biology | Year: 2012

Heterochromatin is important for genome integrity and stabilization of gene-expression programs. We have identified the transcription factors Pax3 and Pax9 as redundant regulators of mouse heterochromatin, as they repress RNA output from major satellite repeats by associating with DNA within pericentric heterochromatin. Simultaneous depletion of Pax3 and Pax9 resulted in dramatic derepression of major satellite transcripts, persistent impairment of heterochromatic marks and defects in chromosome segregation. Genome-wide analyses of methylated histone H3 at Lys9 showed enrichment at intergenic major satellite repeats only when these sequences retained intact binding sites for Pax and other transcription factors. Additionally, bioinformatic interrogation of all histone methyltransferase Suv39h-dependent heterochromatic repeat regions in the mouse genome revealed a high concordance with the presence of transcription factor binding sites. These data define a general model in which reiterated arrangement of transcription factor binding sites within repeat sequences is an intrinsic mechanism of the formation of heterochromatin. © 2012 Nature America, Inc. All rights reserved.


Weichsel J.,University of Heidelberg | Urban E.,Institute of Molecular Biotechnology | Small J.V.,Institute of Molecular Biotechnology | Schwarz U.S.,University of Heidelberg
Cytometry Part A | Year: 2012

Migration of motile cells on flat substrates is usually driven by the polymerization of a flat actin filament network. Theoretical models have made different predictions regarding the distribution of the filament orientation in the lamellipodium with respect to the direction of motion. Here we show how one can automatically reconstruct the orientation distribution of actin filaments in the lamellipodium of migrating keratocytes from electron microscopy tomography data. We use two different image analysis methods, an algorithm which explicitly extracts an abstract network representation and an analysis of the gray scale information based on the structure tensor. We show that the two approaches give similar results, both for simulated data and for electron microscopy tomography data from migrating keratocytes. For the lamellipodium at the leading edge of fast moving cells, we find an orientation distribution that is peaked at +35/-35 degrees. For the lamellipodium at the leading edge of slow moving cells as well as for the lamellipodium at the flanks of fast moving cells, one broad peak around 0 degree dominates the distribution. © 2012 International Society for Advancement of Cytometry.


Hasanovic A.,University of Vienna | Winkler R.,University of Vienna | Resch G.P.,Institute of Molecular Biotechnology | Valenta C.,University of Vienna
European Journal of Pharmaceutics and Biopharmaceutics | Year: 2011

The stratum corneum (SC), top layer of the epidermis, is comprised mostly of lipids that are responsible for the permeability properties of the SC and which protect the body from external agents. Changes in these skin microconstituents can be understood by instrumental methods such as attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy. The present work shows that different types of analyzed skin, dermatomed abdominal porcine skin, pig ear skin, and human heat separated skin, influenced both the shape and the intensity of recorded spectra. The typical FTIR spectral bands of the conformation of the lipid aliphatic chains in the skin samples were altered after treatment with pure DPPC liposomes and chitosan (CS) coated DPPC liposomes, but not with aqueous CS-solution. The conformational change could be the reason for the variable permeability of the skin. This was confirmed by tape stripping on pig ear skin (imitating in vivo studies): the amount of aciclovir penetrating from polymer coated and polymer free liposomes was significantly higher under the skin surface in comparison with the aqueous CS-solution. Moreover, the addition of the polymer to liposomes induced a higher skin penetration than pure liposomes. One explanation might be the CS's stronger adhesion to the skin. © 2011 Elsevier B.V. All rights reserved.


Oudit G.Y.,University of Alberta | Penninger J.M.,Institute of Molecular Biotechnology
Current Heart Failure Reports | Year: 2011

Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase that metabolizes several peptides, including the degradation of angiotensin (Ang) II, a peptide with vasoconstrictive/proliferative effects, to generate Ang 1-7, which exerts vasodilatory/antiproliferative actions by acting through its receptor Mas. ACE2 is a multifunctional enzyme, and its actions on other vasoactive peptides, including the apelin-13 and apelin-17 peptides, also can contribute to its cardiovascular effects. The classical pathway of the renin-angiotensin system involving the ACE-Ang II-Ang II type-1 receptor axis is antagonized by the second arm constituted by the ACE2/Ang 1-7/Mas receptor axis. Loss of ACE2 enhances the adverse pathological remodeling susceptibility to pressure overload and myocardial infarction. Human recombinant ACE2 also is a negative regulator of Ang II-induced myocardial hypertrophy, fibrosis, and diastolic dysfunction and suppresses pressure overload-induced heart failure. Due to its characteristics, the ACE2/Ang 1-7/Mas axis may represent new possibilities for developing novel therapeutic strategies for the treatment of hypertension and heart failure. This review summarizes the beneficial effects of ACE2 in heart disease and the potential use of human recombinant ACE2 as a novel therapy for heart failure. © Springer Science+Business Media, LLC 2011.


Urban E.,Institute of Molecular Biotechnology | Jacob S.,Institute of Molecular Biotechnology | Nemethova M.,Institute of Molecular Biotechnology | Resch G.P.,Institute of Molecular Biotechnology | And 2 more authors.
Nature Cell Biology | Year: 2010

Eukaryotic cells can initiate movement using the forces exerted by polymerizing actin filaments to extend lamellipodial and filopodial protrusions. In the current model, actin filaments in lamellipodia are organized in a branched, dendritic network. We applied electron tomography to vitreously frozen 'live' cells, fixed cells and cytoskeletons, embedded in vitreous ice or in deep-negative stain. In lamellipodia from four cell types, including rapidly migrating fish keratocytes, we found that actin filaments are almost exclusively unbranched. The vast majority of apparent filament junctions proved to be overlapping filaments, rather than branched end-to-side junctions. Analysis of the tomograms revealed that actin filaments terminate at the membrane interface within a zone several hundred nanometres wide at the lamellipodium front, and yielded the first direct measurements of filament densities. Actin filament pairs were also identified as lamellipodium components and bundle precursors. These data provide a new structural basis for understanding actin-driven protrusion during cell migration. © 2010 Macmillan Publishers Limited. All rights reserved.


Metze S.,University of Bern | Herzog V.A.,University of Bern | Herzog V.A.,Institute of Molecular Biotechnology | Ruepp M.-D.,University of Bern | Muhlemann O.,University of Bern
RNA | Year: 2013

Nonsense-mediated mRNA decay (NMD) is a eukaryotic post-transcriptional gene regulation mechanism that eliminates mRNAs with the termination codon (TC) located in an unfavorable environment for efficient translation termination. The best-studied NMD-targeted mRNAs contain premature termination codons (PTCs); however, NMD regulates even many physiological mRNAs. An exon-junction complex (EJC) located downstream from a TC acts as an NMD-enhancing signal, but is not generally required for NMD. Here, we compared these "EJC-enhanced" and "EJC-independent" modes of NMD with regard to their requirement for seven known NMD factors in human cells using two well-characterized NMD reporter genes (immunoglobulin μ and β-Globin) with or without an intron downstream from the PTC. We show that both NMD modes depend on UPF1 and SMG1, but detected transcript-specific differences with respect to the requirement for UPF2 and UPF3b, consistent with previously reported UPF2- and UPF3-independent branches of NMD. In addition and contrary to expectation, a higher sensitivity of EJC-independent NMD to reduced UPF2 and UPF3b concentrations was observed. Our data further revealed a redundancy of the endo- and exonucleolytic mRNA degradation pathways in both modes of NMD. Moreover, the relative contributions of both decay pathways differed between the reporters, with PTC-containing immunoglobulin μ transcripts being preferentially subjected to SMG6-mediated endonucleolytic cleavage, whereas β-Globin transcripts were predominantly degraded by the SMG5/SMG7-dependent pathway. Overall, the surprising heterogeneity observed with only two NMD reporter pairs suggests the existence of several mechanistically distinct branches of NMD in human cells. © 2013; Published by Cold Spring Harbor Laboratory Press for the RNA Society.


Kumari S.,University of Cologne | Redouane Y.,Institute of Molecular Biotechnology | Lopez-Mosqueda J.,Goethe University Frankfurt | Shiraishi R.,Institute of Molecular Biotechnology | And 7 more authors.
eLife | Year: 2014

Linear Ubiquitin chain Assembly Complex (LUBAC) is an E3 ligase complex that generates linear ubiquitin chains and is important for tumour necrosis factor (TNF) signaling activation. Mice lacking Sharpin, a critical subunit of LUBAC, spontaneously develop inflammatory lesions in the skin and other organs. Here we show that TNF receptor 1 (TNFR1)-associated death domain (TRADD)-dependent TNFR1 signaling in epidermal keratinocytes drives skin inflammation in Sharpin-deficient mice. Epidermis-restricted ablation of Fas-associated protein with death domain (FADD) combined with receptor-interacting protein kinase 3 (RIPK3) deficiency fully prevented skin inflammation, while single RIPK3 deficiency only delayed and partly ameliorated lesion development in Sharpin-deficient mice, showing that inflammation is primarily driven by TRADD- and FADD-dependent keratinocyte apoptosis while necroptosis plays a minor role. At the cellular level, Sharpin deficiency sensitized primary murine keratinocytes, human keratinocytes, and mouse embryonic fibroblasts to TNF-induced apoptosis. Depletion of FADD or TRADD in Sharpin-deficient HaCaT cells suppressed TNF-induced apoptosis, indicating the importance of FADD and TRADD in Sharpin-dependent anti-apoptosis signaling in keratinocytes.

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