Basel, Switzerland

The Friedrich Miescher Institute for Biomedical Research is a world-class center for basic research in life science based in Basel, Switzerland. Wikipedia.


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Zhu P.,Friedrich Miescher Institute for Biomedical Research
Nature protocols | Year: 2012

Optogenetic approaches allow the manipulation of neuronal activity patterns in space and time by light, particularly in small animals such as zebrafish. However, most techniques cannot control neuronal activity independently at different locations. Here we describe equipment and provide a protocol for single-photon patterned optical stimulation of neurons using a digital micromirror device (DMD). This method can create arbitrary spatiotemporal light patterns with spatial and temporal resolutions in the micrometer and submillisecond range, respectively. Different options to integrate a DMD into a multiphoton microscope are presented and compared. We also describe an ex vivo preparation of the adult zebrafish head that greatly facilitates optogenetic and other experiments. After assembly, the initial alignment takes about one day and the zebrafish preparation takes <30 min. The method has previously been used to activate channelrhodopsin-2 and manipulate oscillatory synchrony among spatially distributed neurons in the zebrafish olfactory bulb. It can be adapted easily to a wide range of other species, optogenetic probes and scientific applications.


Schubeler D.,Friedrich Miescher Institute for Biomedical Research | Schubeler D.,University of Basel
Nature | Year: 2015

Cytosine methylation is a DNA modification generally associated with transcriptional silencing. Factors that regulate methylation have been linked to human disease, yet how they contribute to malignances remains largely unknown. Genomic maps of DNA methylation have revealed unexpected dynamics at gene regulatory regions, including active demethylation by TET proteins at binding sites for transcription factors. These observations indicate that the underlying DNA sequence largely accounts for local patterns of methylation. As a result, this mark is highly informative when studying gene regulation in normal and diseased cells, and it can potentially function as a biomarker. Although these findings challenge the view that methylation is generally instructive for gene silencing, several open questions remain, including how methylation is targeted and recognized and in what context it affects genome readout. © 2015 Macmillan Publishers Limited.


Schubeler D.,Friedrich Miescher Institute for Biomedical Research
Science | Year: 2012

Mammalian methylomes reveal how DNA methylation is infl uenced by the underlying nucleotide sequence.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2014 | Award Amount: 2.20M | Year: 2016

Specificity in the ubiquitin-proteasome system is largely conferred by ubiquitin E3 ligases (E3s). Cullin-RING ligases (CRLs), constituting ~30% of all E3s in humans, mediate the ubiquitination of ~20% of the proteins degraded by the proteasome. CRLs are divided into seven families based on their cullin constituent. Each cullin binds a RING domain protein, and a vast repertoire of adaptor/substrate receptor modules, collectively creating more than 200 distinct CRLs. All CRLs are regulated by the COP9 signalosome (CSN), an eight-protein isopeptidase that removes the covalently attached activator, NEDD8, from the cullin. Independent of NEDD8 cleavage, CSN forms protective complexes with CRLs, which prevents destructive auto-ubiquitination. The integrity of the CSN-CRL system is crucially important for the normal cell physiology. Based on our previous work on CRL structures (Fischer, et al., Nature 2014; Fischer, et al., Cell 2011) and that of isolated CSN (Lingaraju et al., Nature 2014), We now intend to provide the underlying molecular mechanism of CRL regulation by CSN. Structural insights at atomic resolution, combined with in vitro and in vivo functional studies are designed to reveal (i) how the signalosome deneddylates and maintains the bound ligases in an inactive state, (ii) how the multiple CSN subunits bind to structurally diverse CRLs, and (iii) how CSN is itself subject to regulation by post-translational modifications or additional further factors. The ERC funding would allow my lab to pursue an ambitious interdisciplinary approach combining X-ray crystallography, cryo-electron microscopy, biochemistry and cell biology. This is expected to provide a unique molecular understanding of CSN action. Beyond ubiquitination, insight into this >13- subunit CSN-CRL assembly will allow examining general principles of multi-subunit complex action and reveal how the numerous, often essential, subunits contribute to complex function.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-COG | Phase: ERC-CoG-2015 | Award Amount: 2.00M | Year: 2017

RNAi refers to the ability of small RNAs to silence expression of homologous sequences. A surprising link between epigenetics and RNAi was discovered more than a decade ago, and I was fortunate enough to be involved in this exciting field of research from the beginning. It is now well established that endogenous small RNAs have a direct impact on the genome in various organisms. Yet, the initiation of chromatin modifications in trans by exogenously introduced small RNAs has been inherently difficult to achieve in all eukaryotic cells. This has sparked controversy about the importance and conservation of RNAi-mediated epigenome regulation and hampered systematic mechanistic dissection of this phenomenon. Using fission yeast, we have discovered a counter-acting mechanism that impedes small RNA-directed formation of heterochromatin and constitutes the foundation of this proposal. Our goal is to close several knowledge gaps and test the intriguing possibility that the suppressive mechanism we discovered is conserved in mammalian cells. We will employ yeast and embryonic stem cells and use cutting-edge technologies (i.e., chemical mutagenesis combined with whole-genome sequencing, genome editing with engineered nucleases, and single-cell RNA sequencing) to address fundamental, as yet unanswered questions. My proposal consists of four major aims. In aim 1, I propose to use proteomics approaches and to perform yeast genetic screens to define additional pathway components and regulatory factors. Aim 2 builds on our ability to finally trigger de novo formation of heterochromatin by synthetic siRNAs acting in trans, addressing many of the outstanding mechanistic questions that could not be addressed in the past. In Aims 3 and 4, experiments conducted in yeast and mouse cells will elucidate missing fragments critical to our understanding of the conserved principles behind RNAi-mediated epigenetic gene regulation.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2014 | Award Amount: 2.50M | Year: 2016

The project outlined here addresses the fundamental question how the brain encodes and controls behavior. While we have a reasonable understanding of the role of entire brain areas in such processes, and of mechanisms at the molecular and synaptic levels, there is a big gap in our knowledge of how behavior is controlled at the level of defined neuronal circuits. In natural environments, chances for survival depend on learning about possible aversive and appetitive outcomes and on the appropriate behavioral responses. Most studies addressing the underlying mechanisms at the level of neuronal circuits have focused on aversive learning, such as in Pavlovian fear conditioning. Understanding how activity in defined neuronal circuits mediates appetitive learning, as well as how these circuitries are shared and interact with aversive learning circuits, is a central question in the neuroscience of learning and memory and the focus of this grant application. Using a multidisciplinary approach in mice, combining behavioral, in vivo and in vitro electrophysiological, imaging, optogenetic and state-of-the-art viral circuit tracing techniques, we aim at dissecting the neuronal circuitry of appetitive Pavlovian conditioning with a focus on the amygdala, a key brain region important for both aversive and appetitive learning. Ultimately, elucidating these mechanisms at the level of defined neurons and circuits is fundamental not only for an understanding of memory processes in the brain in general, but also to inform a mechanistic approach to psychiatric conditions associated with amygdala dysfunction and dysregulated emotional responses including anxiety and mood disorders.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2015 | Award Amount: 2.50M | Year: 2016

Breast cancer is diagnosed in ~1.4 million women worldwide and ~500,000 lives are lost to the disease annually. Patients may do well after surgery and initial treatment, but drug resistant and fatal metastases often develop. Improved treatment options are urgently needed. The connecting thread of this project is the identification of epigenetic drivers of breast cell fate, tumor heterogeneity and metastasis. Tumor heterogeneity impinges on prognosis, response to therapy, and metastasis and is one of the most important and clinically relevant areas of cancer research. Tumor heterogeneity results from genetic and epigenetic alterations that enhance the plasticity and fitness of cancer cells in the face of hurdles like the metastatic cascade and anti-cancer therapies. Unfortunately, the driving molecular mechanisms remain unclear, particularly the potential interplay between signalling pathways and epigenetic programs. This interdisciplinary project uses pathophysiologically relevant models and state-of-the-art technologies to identify molecular mechanisms underlying crosstalk between key signalling pathways and epigenetic programs in the normal and neoplastic breast. We hypothesize that interfering with these programs will decrease tumor heterogeneity. We will address the effects of: - SHP2/ERK signalling on the epigenetic programs of tumor-initiating cells (Aim 1) - PI3K pathway hyperactivation on the epigenetic programs underpinning cell plasticity (Aim 2) - Epigenetic regulators on normal mammary cell self-renewal and on metastasis (Aim 3) By investigating the integrated effects of key signalling pathways and epigenetic programs in normal and neoplastic breast, this multipronged project will identify and validate mechanisms of cell plasticity. The derived mechanistic understanding will generate means to interfere with tumor heterogeneity and thus improve the efficacy of anti-cancer therapies and ultimately the clinical outcome for patients with breast cancer.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2015 | Award Amount: 2.50M | Year: 2016

Nervous systems produce adaptive behavior, arguably their most important function, through learning and memory. Memories ensure that what is learned will be available for later retrieval. Upon the initial learning process, synaptic plasticity important for memory consolidation is triggered within minutes, but whether, and in which form memories will be retained more permanently can be influenced by information and insights gained after the initial trigger. Learning and memory have been studied extensively, but we still know very little about the mechanisms through which memories are shaped after acquisition. Here we hypothesize that instead of simply reflecting requirements to produce long-term memory traces, cascades of plasticity processes induced at the time of acquisition might also reflect systems requirements for updating of new relevant information, as well as selection of potentially useful memories that need to enter the process of long-term consolidation. Recent advances in neuroscience have provided powerful novel means to reveal, analyze and manipulate memory traces in the living brain, from single neurons to systems, and to interrogate their function. This research program will address the functional roles of learning-related plasticity processes unfolding subsequent to acquisition in learning and memory. We will investigate how hippocampal memories are shaped during several hours after acquisition through network activity and addition of new information through experience, and how these processes involve unique roles for dorsal hippocampus, and for dedicated neuronal circuits. Furthermore, we will study how shaped memories are then long-term consolidated, including the key role of ventral hippocampal circuitry, and how memories are further modified through subsequent learning. This research will produce fundamentally novel insights into how learning leads to adaptive behavior through writing and editing of memories.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2015 | Award Amount: 2.50M | Year: 2016

Movement is the behavioral output of the nervous system. Animals carry out an enormous repertoire of distinct actions, spanning from seemingly simple repetitive tasks like walking to much more complex movements such as forelimb manipulation tasks. An important question is how neuronal circuits are organized and function to choose, maintain, adjust and terminate these many distinct motor behaviors. Recent technological advances in neuroscience have made it possible to begin to unravel the links between the organization of specific neuronal circuit elements in the CNS and the control of movement, a topic that will be central to this research program. While past work proposes that supraspinal centers in the brainstem are instrumental to the control of action diversification, little is known about how brainstem circuits translate movement intention to body control, how competing motor programs are selected, and how behavioral state influences movement control. The goal of this research project is to unravel the circuit blueprint of mouse descending motor pathways at a fine-scale level and to probe the intersection between revealed circuit organization and their behavioral function at many levels. The focus will be on studies on the interactions between brainstem neurons and spinal circuits to determine how initiation, duration, termination and selection of motor programs are implemented through specific neuronal subpopulations. Mapping descending connectivity matrices of motor circuits will serve as entry point and we will make use of state-of-the art intersectional technology including mouse genetics, viral approaches, in vivo neuronal recordings and activity manipulations of specific neuronal populations during behavior. Together, our project will elucidate the circuit organization and function of the descending motor output system and thereby uncover principles of how the nervous system generates diverse actions.


Grant
Agency: Cordis | Branch: H2020 | Program: ERC-ADG | Phase: ERC-ADG-2015 | Award Amount: 2.86M | Year: 2016

In mammals, fusion of two highly differentiated gametes gives rise to a totipotent zygote capable of developing into a whole organism. It coincides with translation and degradation of maternally provided transcripts, initiation of global transcription called zygotic genome activation (ZGA), and epigenetic reprogramming of germline chromatin states into an embryonic state. The molecular mechanisms underlying this exquisite reprogramming of cell fate are barely understood. This research program has the ambitious goal to identify and characterize in a comprehensive way the transcription factors and chromatin regulators which initiate and regulate ZGA in a parental specific manner in early mouse embryos. We will utilize novel and highly sensitive genomic approaches to measure nascent transcription and determine open and modified chromatin landscapes in oocytes and early embryos, wild-type and conditionally deficient for major epigenetic modifiers. We will apply computational approaches to identify candidate TFs and histone modifiers controlling ZGA. We will use molecular and developmental biology approaches, combined with sensitive quantitative live-imaging, to interrogate the function of TFs and their binding sites for ZGA. We will further investigate the significance of possible paternal inheritance of nucleosomes at CpG islands for gene regulation during ZGA and later development by depleting nucleosomes from mature sperm by using sophisticated conditional deficiency and gain-of-function mouse models. By transferring nuclei of immature spermatid and mature sperm into oocytes, we will interrogate the relevance of nucleosome eviction during spermatogenesis, as a possibly truly epigenetic reprogramming process, for defining embryonic competence. ERC funding would represent a crucial contribution to dissecting the molecular mechanisms underlying acquisition of totipotency in mouse embryos and may impact on the use of Assisted Reproductive Technologies in human med

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