Epigenetic regulation of enhancer activity in the mammalian genome

Cell types are defined by their spatiotemporal gene expression patterns and their differential activity of promoters and enhancers. Enhancers are cis-regulatory elements in the DNA critical for the acquisition and maintenance of cellular identities by regulating the expression of key genes. Enhancers serve as landing pads for transcription factors (TFs) which are DNA-binding proteins that interpret the genomic code and enhance gene expression upon their binding. However, the underlying DNA sequence does not solely convey binding specificity, and therefore it is still largely elusive what additional factors regulate TF binding. An important regulatory layer in gene expression are dynamic and reversible epigenetic modifications of chromatin including DNA and histone proteins. To date, dozens of histone modifications have been identified that are associated with different genomic contexts and transcriptional states. For instance, histone H3 lysine acetylation has been generally associated with active chromatin as active enhancers and promoters, while histone H3 tri-methylation at lysine 23 (H3K27me3) is coupled to transcription repression. Yet, the causal contribution of such histone modifications to the regulation of enhancer activity and TF binding is still large unknown. To address this question, I developed a technical approach to analyse TF binding at DNA molecules where a certain histone modification of interest is present. For this, I combined a genomic enrichment technique with a single molecule footprinting (SMF) approach that allows to detect TF binding at single DNA molecule resolution. However, this experimental set-up paired with different optimization approaches did not produce high enough enrichments of DNA molecules harboring certain histone modifications to suffice the required statistical power. Therefore, the focus was laid on investigating the causal role of DNA methylation. DNA methylation in CpG context is the most common epigenetic modification in the mammalian genome that covers 70-80% of all CpG dinucleotides. Despite its prevalence, DNA methylation can be highly dynamic, especially at enhancer elements that exhibit reduced methylation levels during their activation. Previous studies have identified that the binding of TFs to enhancers is correlated with the partial loss in DNA methylation and it has been suggested that DNA methylation regulates enhancer activity. This hypothesis has remained elusive up to date, which has multiple reasons. First, the relationship between TFs and DNA methylation is bidirectional. Previous studies have identified many methyl-sensitive TFs in vitro whose binding is reduced upon methylation of their DNA binding motif. Some of those have been confirmed by in vivo studies, which showed that DNA methylation prevents the spurious binding of those TFs in the genome. Opposingly, TFs have also been identified to be directly responsible for the demethylation of enhancers. In consequence, the bidirectional regulation between DNA methylation and TF binding has prevented the establishment of a causal relationship between them. Second, the cell-to-cell epigenetic variability observed as intermediate methylation at enhancers elements makes common bulk-cell genomics approaches ineffective to identify a direct correlation between DNA methylation and TF binding and to determine whether DNA methylation generally contributes to the regulation of enhancer activity. In the here presented PhD project, I overcame these issues and limitation by advancing the single molecule footprinting (SMF) approach to resolve chromatin accessibility, TF binding, and simultaneously quantify the presence of DNA methylation on the same DNA molecules. By applying this technology across the murine genome, I demonstrate that TFs can bind most (>90%) enhancers irrespective of the underlying DNA methylation, suggesting that presence of DNA methylation does not generally impede enhancer activity. Yet, for stem cells and three somatic cell types, I identified active enhancers where TF occupancy is directly repressed by DNA methylation, including enhancers involved in the control of key cell identity genes. Using global perturbation assays and orthogonal enhancer activity measurements, I was able to show that at these active sites, DNA methylation directly controls the occupancy levels of TFs such as Max-Myc, that play a key role in the control of stem cell identity and proliferation. In the end, my data suggest a model where the function of DNA methylation extends beyond protecting the genome from spurious TF binding, by directly regulating the activation of cell-type specific enhancers. This detailed analysis is an important addition to our general knowledge on gene regulation and suggest that while epigenetic factors may have largely redundant functions, their individual contributions can play important and instructive roles in tuning the quantitative expression of key cell- specific genes. Understanding the regulation of such genes involved in cell identity will have important implications in the comprehension of development and disease

IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions

Babraham Institute Translational Advisory Group award (to M.E.-M. and F.v.M.); M.E.-M. is supported by a BBSRC Discovery Fellowship [BB/T009713/1]; EMBO Fellowship [ALTF938-2014]; Marie Sklodowska-Curie Individual Fellowship; Work in S.T.d.R.’s team at iMM JLA was supported by Fundac¸ao para a Ci ˜ encia e Tecnologia ˆ(FCT) Ministerio da Cincia, Tecnologia e Ensino Supe- ˆrior (MCTES), Portugal [PTDC/BEX-BCM/2612/2014, PTDC/BIA-MOL/29320/2017 IC&DT]; S.T.d.R. has a CEECUIND/01234/207 assistant research contract from FCT/MCTES; T.K.’s work was supported by Erasmus+and University Foundation of eng. Lenarciˇ c Milan at ˇthe University of Ljubljana. Funding for open access charge: accounts payable, Babraham Institute.publishersversionpublishe

Panta Rhei benchmark dataset: socio-hydrological data of paired events of floods and droughts

As the adverse impacts of hydrological extremes increase in many regions of the world, a better understanding of the drivers of changes in risk and impacts is essential for effective flood and drought risk management and climate adaptation. However, there is currently a lack of comprehensive, empirical data about the processes, interactions and feedbacks in complex human-water systems leading to flood and drought impacts. Here we present a benchmark dataset containing socio-hydrological data of paired events, i.e., two floods or two droughts that occurred in the same area. The 45 paired events occurred in 42 different study areas and cover a wide range of socio-economic and hydro-climatic conditions. The dataset is unique in covering both floods and droughts, in the number of cases assessed, and in the quantity of socio-hydrological data. The benchmark dataset comprises: 1) detailed review style reports about the events and key processes between the two events of a pair; 2) the key data table containing variables that assess the indicators which characterise management shortcomings, hazard, exposure, vulnerability and impacts of all events; 3) a table of the indicators-of-change that indicate the differences between the first and second event of a pair. The advantages of the dataset are that it enables comparative analyses across all the paired events based on the indicators-of-change and allows for detailed context- and location-specific assessments based on the extensive data and reports of the individual study areas. The dataset can be used by the scientific community for exploratory data analyses e.g. focused on causal links between risk management, changes in hazard, exposure and vulnerability and flood or drought impacts. The data can also be used for the development, calibration and validation of socio-hydrological models. The dataset is available to the public through the GFZ Data Services (Kreibich et al. 2023, link for review: https://dataservices.gfz-potsdam.de/panmetaworks/review/923c14519deb04f83815ce108b48dd2581d57b90ce069bec9c948361028b8c85/).</p

Easter Eggs and Other Cocoa (Theobroma cacao L) Products Quality: Insects, Mites, Fungi and Packaging versus Critical Control Points

Abstract The samples collected were sold in Florianopolis, Southern Brazil, an

The need to integrate flood and drought disaster risk reduction strategies

Most research on hydrological risks focuses either on flood risk or drought risk, whilst floods and droughts are two extremes of the same hydrological cycle. To better design disaster risk reduction (DRR) measures and strategies, it is important to consider interactions between these closely linked phenomena. We show examples of: (a) how flood or drought DRR measures can have (unintended) positive or negative impacts on risk of the opposite hazard; and (b) how flood or drought DRR measures can be negatively impacted by the opposite hazard. We focus on dikes and levees, dams, stormwater control and upstream measures, subsurface storage, migration, agricultural practices, and vulnerability and preparedness. We identify key challenges for moving towards a more holistic risk management approach

ტასო და ვასო აბაშიძეები

peer reviewedMost research on hydrological risks focuses either on flood risk or drought risk, whilst floods and droughts are two extremes of the same hydrological cycle. To better design disaster risk reduction (DRR) measures and strategies, it is important to consider interactions between these closely linked phenomena. We show examples of: how flood or drought DRR measures can have (unintentional) positive or negative impacts on risk of the opposite hazard; and (b) how flood or drought DRR measures can be negatively impacted by the opposite hazard. We focus on dikes and levees, dams, stormwater control and upstream measures, subsurface storage, migration, agricultural practices, and vulnerability and preparedness. We identify key challenges for moving towards a more holistic risk management approach

The challenge of unprecedented floods and droughts in risk management.

Risk management has reduced vulnerability to floods and droughts globally1,2, yet their impacts are still increasing3. An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data4,5. On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change3

The challenge of unprecedented floods and droughts in risk management

International audienceAbstract Risk management has reduced vulnerability to floods and droughts globally 1,2 , yet their impacts are still increasing 3 . An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data 4,5 . On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change 3