ERC FUNDED PROJECTS

"I propose a systematic study of the type of genetic variation enabling adaptation and factors that limit rates of adaptation in natural populations. New methods will be developed for analysing data from experimental evolution and population genomics. The methods will be applied to state of the art data from both fields. Adaptation is generated by natural selection sieving through heritable variation. Examples of adaptation are available from the fossil record and from extant populations. Genomic studies have supplied many instances of genomic regions exhibiting footprint of natural selection favouring new variants. Despite ample proof that adaptation happens, we know little about beneficial mutations– the raw stuff enabling adaptation. Is adaptation mediated by genetic variation pre-existing in the population, or by variation supplied de novo through mutations? We know even less about what factors limit rates of adaptation. Answers to these questions are crucial for Evolutionary Biology, but also for believable quantifications of the evolutionary potential of populations. Population genetic theory makes predictions and allows inference from the patterns of polymorphism within species and divergence between species. Yet models specifying the fitness effects of mutations are often missing. Fitness landscape models will be mobilized to fill this gap and develop methods for inferring the distribution of fitness effects and factors governing rates of adaptation. Insights into the processes underlying adaptation will thus be gained from experimental evolution and population genomics data. The applicability of insights gained from experimental evolution to comprehend adaptation in nature will be scrutinized. We will unite two very different approaches for studying adaptation. The project will boost our understanding of how selection shapes genomes and open the way for further quantitative tests of theories of adaptation."

1 159 857 €

Start date: 2013-04-01, End date: 2018-03-31

Cancer and other diseases are driven by genomic alterations initiated by DNA breaks. Within our genomes, some regions are particularly prone to breakage, and these are known as common fragile sites (CFSs). CFSs are present in every person and are frequently sites of oncogenic chromosomal rearrangements. Intriguingly, despite their fragility, many CFSs are well conserved through evolution, suggesting that these regions have important physiological functions that remain elusive. My previous background in genome editing, proteomics and replication-born DNA damage has given me the tools to propose an ambitious and comprehensive plan that tackles fundamental questions on the biology of CFSs. First, we will perform a systematic analysis of the function of CFSs. Most of the CFSs contain very large genes, which has made technically difficult to dissect whether the CFS role is due to the locus itself or to the encoded gene product. However, the emergence of the CRISPR/Cas9 technology now enables the study of CFSs on a more systematic basis. We will pioneer the engineering of mammalian models harbouring large deletions at CFS loci to investigate their physiological functions at the cellular and organism levels. For those CFSs that contain genes, the cDNAs will be re-introduced at a distal locus. Using this strategy, we will be able to achieve the first comprehensive characterization of CFS roles. Second, we will develop novel targeted approaches to interrogate the chromatin-bound proteome of CFSs and its dynamics during DNA replication. Finally, and given that CFS fragility is influenced both by cell cycle checkpoints and dNTP availability, we will use mouse models to study the impact of ATR/CHK1 pathway and dNTP levels on CFS instability and cancer. Taken together, I propose an ambitious, yet feasible, project to functionally annotate and characterise these poorly understood regions of the human genome, with important potential implications for improving human health.

1 499 711 €

Start date: 2016-05-01, End date: 2021-04-30

Vitamin A supplementation (VAS) and vaccines are the most powerful tools to reduce child mortality in low-income countries. However, we may not use these interventions optimally because we disregard that the interventions may have immunomodulatory effects which differ for boys and girls and which may interact with the effects of other interventions. I have proposed the hypothesis that VAS and vaccines interact. This hypothesis is supported by randomised and observational studies showing that the combination of VAS and DTP may be harmful. I have furthermore proposed that VAS has sex-differential effects. VAS seems beneficial for boys but may not carry any benefits for girls. These findings challenge the current understanding that VAS and vaccines have only targeted effects and can be given together without considering interactions. This is of outmost importance for policy makers. The global trend is to combine health interventions for logistic reasons. My research suggests that this may not always be a good idea. Furthermore, the concept of sex-differential response to our common health interventions opens up for a completely new understanding of the immunology of the two sexes and may imply that we need to treat the two sexes differently in order to treat them optimally possibly also in high-income countries. In the present proposal I outline a series of inter-disciplinary epidemiological and immunological studies, which will serve to determine the overall and sex-differential effects of VAS and vaccines, the mechanisms behind these effects, and the basis for the immunological difference between boys and girls. If my hypotheses are true we can use the existing tools in a more optimal way to reduce child mortality without increasing costs. Thus, the results could lead to shifts in policy as well as paradigms.

1 686 043 €

Start date: 2010-01-01, End date: 2014-12-31

Inheritance of DNA sequence and its proper organization into chromatin is fundamental for eukaryotic life. The challenge of propagating genetic and epigenetic information is met in S phase and entails genome-wide disruption and restoration of chromatin coupled to faithful copying of DNA. How specific chromatin structures are restored on new DNA and transmitted through mitotic cell division remains a fundamental question in biology central to understand cell fate and identity. Chromatin restoration on new DNA involves a complex set of events including nucleosome assembly and remodelling, restoration of marks on DNA and histones, deposition of histone variants and establishment of higher order chromosomal structures including sister-chromatid cohesion. To dissect these fundamental processes and their coordination in time and space with DNA replication, we have developed a novel technology termed nascent chromatin capture (NCC) that provides unique possibility for biochemical and proteomic analysis of chromatin replication in human cells. I propose to apply this innovative cutting-edge technique for a comprehensive characterization of chromatin restoration during DNA replication and to reveal how replication timing and genotoxic stress impact on final chromatin state. This highly topical project brings together the fields of chromatin biology, DNA replication, epigenetics and genome stability and we expect to make groundbreaking discoveries that will improve our understanding of human development, somatic cell reprogramming and complex diseases like cancer. The proposed research will 1) identify and characterize novel mechanisms in chromatin restoration and 2) address molecularly how replication timing and genotoxic insults influence chromatin maturation and final chromatin state.

1 692 737 €

Start date: 2011-11-01, End date: 2017-04-30

Cardiovascular disease, diabetes and cancer have a dramatic impact on modern society, and in great part are related to uptake of cholesterol and sugar. We still know surprisingly little about the molecular details of the processes that goes on in this essential part of human basic metabolism. This application addresses cholesterol and sugar transport and aim to elucidate the molecular mechanism of cholesterol and sugar uptake in humans. It moves the frontiers of the field by shifting the focus to in vitro work allowing hitherto untried structural and biochemical experiments to be performed. Cholesterol uptake from the intestine is mediated by the membrane protein NPC1L1. Despite extensive research, the molecular mechanism of NPC1L1-dependent cholesterol uptake still remains largely unknown. Facilitated sugar transport in humans is made possible by sugar transporters called GLUTs and SWEETs, and every cell possesses these sugar transport systems. For all these uptake systems structural information is sorely lacking to address important mechanistic questions to help elucidate their molecular mechanism. I will address this using a complementary set of methods founded in macromolecular crystallography and electron microscopy to determine the 3-dimensional structures of key players in these uptake systems. My unpublished preliminary results have established the feasibility of this approach. This will be followed up by biochemical characterization of the molecular mechanism in vitro and in silico. This high risk/high reward membrane protein proposal could lead to a breakthrough in how we approach human biochemical pathways that are linked to trans-membrane transport. An improved understanding of cholesterol and sugar homeostasis has tremendous potential for improving general public health, and furthermore this proposal will help to uncover general principles of endocytotic uptake and facilitated diffusion systems at the molecular level.

1 499 848 €

Start date: 2015-07-01, End date: 2020-06-30

The integrity of a cell's genome is constantly challenged by DNA lesions such as base modifications and DNA strand breaks. A single double-strand break is lethal if unrepaired and may lead to loss-of-heterozygosity, mutations, deletions, genomic rearrangements and chromosome loss if repaired improperly. Such genetic alterations are the main cause of cancer and other genetic diseases. Homologous recombination is an error-free pathway for repairing DNA lesions such as single- and double-strand breaks, and for the restart of collapsed replication forks. This pathway is catalyzed by giga-Dalton protein complexes consisting of dozens of different proteins. These DNA repair factories are able to catalyze complex, multi-step biochemical processes, which have so far failed reconstitution in vitro. The aim of this project is to establish an understanding of how cells catalyze complex biochemical processes such as homologous recombination in vivo. To reach this goal, we will seek to define the complete set of RNA and protein components of DNA repair factories using a combination of genetic, cell biological and biochemical approaches in the yeast Saccharomyces cerevisiae. Further, we will characterize the molecular architecture of DNA repair factories using fluorescence resonance energy transfer (FRET) and by applying systematic hybrid loss-of-heterozygosity (LOH) to physical interactions among DNA repair proteins. Key findings will be extended to metazoans using the chicken DT40 model system. My aim is to determine the fundamental molecular principles that govern protein factories in living cells. As such, our results are likely to be directly relevant to other protein factories such as DNA replication factories, PML bodies, nuclear pore complexes and transcription clusters.

1 700 030 €

Start date: 2009-12-01, End date: 2014-11-30

Understanding the mechanisms underlying the initiation and regulation of transcription remains one of the most fundamental questions in biology. Much of what we know about the transcription process was inferred from experiments on a handful of genes. As these experiments are not realistically scalable, corresponding computational methods building on these findings have emerged; however, these are not accurate enough for annotation of genomes. The limitations reflect that we have no accurate universal model describing transcription initiation; to a large extent, our understanding is based on case stories. Recently, high-throughput methods have been developed to chart the TSS landscape with nucleotide resolution. Using these data, I have dissected promoters at nucleotide level and found patterns that explain the transcription initiation rate for individual nucleotides. The objective for this work is to extend this to the first universal model for how cells select core promoters and associated TSSs. This will have two counterparts: i)prediction of TSSs from DNA sequence given a region of accessible DNA, and ii)prediction of DNA accessibility based on DNA sequences and dynamic epigenetic factors. Such a model will be a corner stone of future experimental and computational transcriptome and gene regulation studies.

812 399 €

Start date: 2008-09-01, End date: 2013-08-31

Domesticated crops hardly resemble their wild ancestors, and often trade higher yield in artificially optimized conditions for lower performance in fluctuating environments. Leafcutter ants (genus Atta) provide fascinating parallels with human farmers, harvesting fresh vegetation used as compost to produce domesticated fungal crops that feed massive societies with millions of workers. However, while human agricultural systems are imperiled by rapid global changes, leafcutter ants have managed to grow one type of cultivar from Texas to Argentina, thriving across extreme rainfall and temperature gradients and across diverse climates over millions of years. However, the eco-physiological mechanisms governing this farming resiliency are poorly understood. I propose a new in vitro mapping paradigm to visualize the niche requirements of fungal cultivars. Creating multidimensional landscapes of nutrient availability (e.g. protein, carbohydrates, Na, P) and environmental stress (e.g. temperature, moisture, plant toxins, crop pathogens) I will answer three main questions: 1) What genes and biochemical pathways shape cultivar performance across interacting gradients of nutrition and stress? 2) Do colonies harvest substrates to navigate nutritional contours of cultivar performance maps and avoid production tradeoffs? 3) Do locally adaptive cultivar traits shape the performance of farming societies across regional ecological gradients, and over 60 million years of co-evolutionary crop domestication by farming ants? My cutting-edge approach will deliver transformative advances to the field of eco-physiology, enabling seamless integration between field and laboratory experiments, and providing new ways to visualize evolutionary mechanisms across levels of biological organization from genes to symbiotic partnerships, and from within diverse farming assemblages to across populations spanning entire continents.

1 427 741 €

Start date: 2018-02-01, End date: 2023-01-31

Due to its remarkable self-renewing capacity, the fly gut has recently become a prime paradigm for studying stem-cell function during adult tissue homeostasis. This capacity for self-renewal relays on the proliferative activity of the intestinal stem cells (ISC), which is tightly coupled with cell loss to maintain intestinal homeostasis. ISC proliferation is controlled by multiple local and systemic signals released from the ISC niche (enterocytes (ECs), enteroendocrine (EE) cells, enteroblasts (EBs), and visceral muscles (VMs)) and non-gastrointestinal (non-GI) organs. Despite the physiological divergence between insects and mammals, studies have shown that flies represent a model that is well suited for studying stem cell physiology during ageing, stress, and infection. As a saturating approach to identify local and systemic signals controlling intestinal homeostasis in steady-state and challenged conditions, RNAis will be used to known down all genes encoding secreted peptides specifically in ECs, EEs, or VMs and all genes encoding transmembrane and membrane-associated proteins in the VMs. The proposed screens should identify novel intra- and inter-organ circuitries allowing communication between the gut and other organs to provide organismal health. In addition, the systematic knockdown of secreted peptides from the ISC niche could identify gut-derived signals that couple changes in environmental inputs, such as nutrient availability, with systemic changes in feeding behavior, energy balance, and metabolism. Since large-scale approaches are not feasible in vertebrate models, the signals identified in the above screens could potentially reveal novel couplings contributing to mammalian GI homeostasis and disease. The final part of the proposed project aims a deciphering the molecular signals coupling epithelial fitness with ligand-independent TNFR activation to control ISC division and epithelial turnover in steady-state, challenged and pathological conditions.

1 498 964 €

Start date: 2019-02-01, End date: 2024-01-31

Maintaining oxygen homeostasis is an essential requirement for all metazoa. Oxygen is required for efficient generation of energy, however, as oxygen levels decrease (hypoxia), cells mount a variety of adaptive responses. Each cell in the body can sense and respond to hypoxia, yet the molecular mechanisms that regulate these responses are only beginning to be delineated. Hypoxia plays crucial roles in the pathophysiology of cancer, neurological dysfunction, myocardial infarction and lung disease. Therefore, the goal of the proposed research is to better understand how cells sense and adapt to hypoxia. To this end, I am using the powerful genetic model of Caenorhabditis elegans to identify novel molecular mechanisms required for oxygen homeostatic responses. A critical regulator of hypoxic responses in all cell types is the conserved hypoxia-inducible factor (HIF-1). In response to a hypoxic insult, HIF-1 transcriptionally regulates a wide variety of target genes to facilitate adaptation. Recent studies indicate that in addition to the canonical HIF-1 pathway, microRNAs (miRNAs) play important roles in hypoxic response mechanisms. miRNAs are regulatory molecules that predominantly repress protein production of their target genes, however, their roles in hypoxic adaptation are poorly understood. I recently found that specific phylogenetically conserved miRNAs are regulated by hypoxia in C. elegans; and that the function of these miRNAs is required for survival of animals in low oxygen conditions. This is truly an emerging field of science and I expect to make groundbreaking discoveries in the regulation of hypoxic and metabolic responses by miRNAs, which will improve our understanding of many disease processes. The proposed research will 1) analyze the functional roles of specific miRNAs in hypoxic responses and 2) utilize immunoprecipitation, bioinformatics and genetic screening combined with state-of-the-art deep sequencing technology to identify novel miRNA targets required for adaptation to hypoxia.

1 478 508 €

Start date: 2010-11-01, End date: 2015-10-31

Drug resistance is limiting our ability to treat most infectious diseases and forms of cancer. Indeed this relentless evolution is the major driver of treatment failure for diseases that are responsible for over half of the global disease related mortality. Yet, the underlying principles that guide this evolutionary response are poorly understood, in particular with regards to understanding the impact of multidrug treatment. LimitMDR will characterize evolutionary trajectories leading to multidrug resistance in response to individual and combination drug treatment through the execution of large-scale adaptive evolution experiment with two bacterial pathogens followed by genome sequencing and phenotyping. This effort will enable testing of contrasting hypotheses regarding the evolution of multidrug resistance in response to combination treatment. We will characterize the cause-and-effect of resistance and sensitivity mutations identified in our global data set and map comprehensive fitness landscapes of mutations accumulated during drug resistance evolution to understand the evolutionary dynamics underlying resistance evolution. To accomplish these bold goals we shall develop novel multiplexed methodologies enabling unprecedented scale of construction and phenotypic testing of identified mutations. While genetic epistasis is considered of key importance to resistance evolution most studies focus on mutations within an individual gene. Through the development of a novel experimental approach we shall elucidate complex epistatic interaction networks between mutations accumulated during resistance evolution. Finally, we will conduct mechanistic studies to uncover the mechanisms of collateral sensitivity. These studies will shed light on this underappreciated phenomenon, which is of critical relevance to drug discovery and the evolution of drug resistance. In conclusion LimitMDR will develop groundbreaking novel methodologies and scientific insights that will c

1 492 453 €

Start date: 2015-05-01, End date: 2020-04-30

The directed control of protein activity plays a crucial role in the regulation of growth and development of multicellular organisms. Different post-translational control mechanisms are known to influence the activity of proteins. Here, I am proposing a novel way to control the activity of proteins that function as multimeric complexes. MicroProteins, are small single-domain protein species that can influence target proteins by sequestering them into non-productive protein complexes. I have developed the concept of microProtein function and subsequently started to identify novel microProtein regulators in the model plant Arabidopsis. The aim of this proposal is to use the microProtein concept and build synthetic microProtein modules in economical import crop plants. By combining synthetic biology approaches with modern plant breeding, we intent to re-wire plant development and alter the flowering behaviour of rice. In addition, we will use a combination of artificial microProteins and microProtein-resistant transcription factors to modify the inclination angle of leaves in rice and the bioenergy model species Brachypodium distachion. Modification of the leaf angle will allow us to grow crops at higher densities, thus having the potential to increase both biomass and seed production per acreage. Finally, we aim to identify novel, evolutionary conserved microProtein-modules and unravel the mechanism of microProtein function, to study their role in plant development and adaptation.

1 443 320 €

Start date: 2013-12-01, End date: 2018-11-30

Targeted chemotherapy in combination with external beam radiation therapy (radiotherapy) is a promising approach to significantly improve the therapeutic outcome for cancer patients. To achieve this, it is essential to develop drug delivery technology that specifically delivers the chemotherapeutic drugs to cancerous tissue. Radiotherapy is an indispensable part of modern cancer treatment; however, despite efforts in improving planning and execution of treatment, the unbalance between therapeutic benefit and side effects limits cure rates, and new approaches are needed to bring to fruition the full potential of radiotherapy. Today, there is considerable focus on systemically administered radiosensitizers for enhancing the effect of radiotherapy and clinical investigations have shown promising results; however, radiosensitizer use is hampered by considerable side effects due to lack of drug targeting to the cancerous tissue. In the first phase of this project, the aim is to develop tumor targeted nanocarrier delivery systems of radiosensitizers to enhance their therapeutic potential and provide a more efficient and site-directed effect of radiotherapy. In the second phase of the project, nanocarriers for tumor specific delivery of checkpoint inhibitors of cancer cell repair mechanisms will be investigated as an additional targeting strategy for sensitizing cancer cells to radiotherapy. The idea is to circumvent cell cycle checkpoints of DNA damage induced by tumor radiation and thereby enhance mitotic catastrophe. This approach will in combination with the delivery of conventional radiosensitizer drugs, further lower the radiation dose needed to induce irreversible damage to cancer cells. Thus, the project aims to develop targeted nanocarriers for high precision delivery of radiosensitizing drugs to cancerous tissue for enhancing the effect of radiotherapy. We aim to demonstrate the applicability and clinical potential of this new approach within the project period

1 498 731 €

Start date: 2013-04-01, End date: 2019-02-28

There have been significant challenges in the research areas of: 1. Foetal PROGramming. The widely use of growth variables as the indicators of foetal environment remains the major methodological limitation. And no research in humans has been able to examine the biomarkers at different programming stages from exposure itself to disease in one single study. 2. Stress. It remains difficult to assess stress and to obtain data on long-term health in a large study. The biological programming effects of prenatal stress need to be elucidated. 3. Bereavement. There is a significant knowledge gap in health of children bereaved by the death of a close relative. 4. Register-based research. To combine the multi-national data is necessary to understand the aetiology and the impact of rare disease and the effects of certain risk factors. But such a first attempt will face many obstacles. The novel approaches in this study are designed to meet all the above challenges. The study uses data from 21 national databases in Denmark, Sweden, and Finland. The first component is a population-based cohort of 6.7 million children. Its objective is to examine the programming effects of an early stress exposure, bereavement during prenatal or early years in life, on a wide range of health outcomes. The second biological component is a proof of concept for foetal programming, examining biomarkers along the pathway from prenatal stress to disease. The study is feasible only in EUROpean settings, which will strengthen the European leadership in epidemiology and public health. It may start a new era for joint European research in public health. The challenges may lead to difficulties and uncertainties for the study, which could also be the source of new scientific insights, hypotheses, and theories.

1 449 950 €

Start date: 2011-01-01, End date: 2016-06-30

There is growing public concern about adverse effects of traffic noise on health, as research has found that traffic noise increases the risk for cardiovascular diseases. Noise is thought to act as a stressor and disturbs sleep. Though this potentially could increase the risk for other major diseases, noise effects on other than the cardiovascular diseases are virtually unexplored. The main objective of this project is to investigate if long-term exposure to road traffic noise is detrimental to various health outcomes in susceptible groups, i.e. children and elderly. Outcomes in children include low birth weight, infections and cognitive performance, and in elderly outcomes include diabetes, cancer, cancer survival, health-related quality of life and health behaviour. The basis of this proposal is two unique Danish cohorts of, respectively, 57,053 elderly and 101,042 children (a national birth cohort). Historic and present residential addresses for all cohort members will be obtained through linkage with the nationwide Central Population Registry, and exposure to road traffic noise and air pollution will be calculated by validated models at all addresses. The health outcomes will be obtained from cohort interviews/questionnaires or found through linkage with unique, nationwide, population-based health registers, such as the Danish National Hospital Registry, the Diabetes Registry and the Cancer Registry. Data will be analysed using a number of statistical analyses depending on design and the character of the endpoint variable. All analyses will be adjusted for potential confounders such as air pollution, smoking and education. Within the EU, 30% of the population lives at locations where the 55dB WHO noise limit is exceeded. Knowledge of harmful effects of noise is, however, limited. The results of the proposed research have a high potential to influence the content and time schedule of noise action plans in the EU member states.

1 334 890 €

Start date: 2012-03-01, End date: 2017-02-28

Enhancers control the correct spatio-temporal activation of gene expression. A comprehensive characterization of the properties and regulatory activities of enhancers as well as their target genes is therefore crucial to understand the regulation and dysregulation of differentiation, homeostasis and cell type specificity. Genome-wide chromatin assays have provided insight into the properties and complex architectures by which enhancers regulate genes, but the understanding of their mechanisms is fragmented and their regulatory targets are mostly unknown. Several factors may confound the inference and interpretation of regulatory enhancer activity. There are likely many kinds of regulatory architectures with distinct levels of output and flexibility. Despite this, most state-of-the-art genome-wide studies only consider a single model. In addition, chromatin-based analysis alone does not provide clear insight into function or activity. This project aims to systematically characterize enhancer architectures and delineate what determines their: (1) restricted spatio-temporal activity; (2) robustness to regulatory genetic variation; and (3) dynamic activities over time. My work has shown enhancer transcription to be the most accurate classifier of enhancer activity to date. This data permits unprecedented modeling of regulatory architectures via enhancer-promoter co-expression linking. Careful computational analysis of such data from appropriate experimental systems has a great potential for distinguishing the different modes of regulation and their functional impact. The outcomes have great potential for providing us with new insights into mechanisms of transcriptional regulation. The results will be particularly relevant to interpretation of regulatory genetic variations. Ultimately, knowing the characteristics and conformations of enhancer architectures will increase our ability to link variation in non-coding DNA to phenotypic outcomes like disease susceptibility.

1 436 293 €

Start date: 2015-05-01, End date: 2020-04-30

Background Lethal epidemics like the Black Death have killed millions of people and must pose an extreme selective pressure on any genetic variant that confers disease protection. Therefore, such epidemics have been hypothesized to play a key role in the evolution of humans. To what extent this is true, is a fundamental question of wide interest. Yet, it remains unanswered, in part due to limitations of the current methods to detect signatures of selection. Objectives I wish to accomplish three linked goals with the proposed project. The first goal is to develop new statistical methods for detecting signatures of adaptive natural selection driven by lethal epidemics. The second goal is to use these new methods to investigate the role of epidemics in recent human evolution by applying them to genetic data from several recent epidemics. The third goal is to gain insights into mechanisms that protect against infectious disease via the identification of genetic variants that have been under selection because they confer disease protection. Methods To reach these goals, extensive simulations will be performed to carefully characterize the genetic signatures of adaptive selection acting on a protective genetic variant during an epidemic. Then new statistical methods that can detect these signatures will be developed. Next, the new methods will be applied to several real datasets, including one from a recent Ebola epidemic. Finally, all signatures of selection detected in these real datasets will be further investigated. Expected outcome and importance This project will deliver new statistical methods that will move the field of selection studies a substantial step beyond the state-of-the-art by filling an important methodological gap. It will also yield key insights into the role of epidemics in recent evolutionary history. Finally, it has the potential to provide new knowledge on the genetics of disease resistance that could help prevent future lethal epidemics.

1 499 600 €

Start date: 2019-01-01, End date: 2023-12-31

Obesity and T2D affect large populations and cause a decline in life expectancy if untreated. The pandemic proportion of obesity and inaptitude of anti-obesity approaches reflect our limited understanding of its complex environmental and genetic etiology. Genome-wide association studies revealed that disease-associated risk variants are often situated in those 98% of the genome not encoding for proteins. This noncoding genomic space yet does not reflect ‘Junk DNA’ but gives rise to >10,000 noncoding RNAs like microRNAs and long, noncoding RNAs (lncRNAs) that implicated in control of glucose metabolism and energy homeostasis also by the applicant (Kornfeld et al. Nature 2013). LncRNAs were paraphrased as 'Dark matter of the genome' due to their tissue-specific and dynamic expression that contrast their poorly understood role in gene regulation. In the 1st part of this proposal, we ask if lncRNAs regulate glucose metabolism and are involved in the obesity-associated dysregulation of insulin signaling in the liver, the major glucoregulatory organ in mammals. Using RNA-Seq and novel lncRNA prediction algorithms, we observed that obesity alters expression of 28 annotated and 15 hitherto unknown lncRNAs in two mouse models of obesity. To identify lncRNAs causally controlling glucose metabolism, we established a siRNA screening system that allows functional interrogation of >650 lncRNAs. These in vitro findings serve as entry for the generation of lncRNA knockout mice that are metabolically phenotyped. In the 2nd part, we hypothesize that germline ncRNAs could control the transgenerational consequences of paternal obesity as shown for lower organisms. This builds upon unpublished findings from our lab showing that obesity profoundly changes expression of germline ncRNAs. In-vitro fertilization and intergenerational breedings will trace the legacy of paternal obesity across generations and reveal ncRNAs involved in this ‘Lamarckian’ control of glucose metabolism.

1 344 498 €

Start date: 2016-05-01, End date: 2021-04-30