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The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum., D.C. was recipient of a fellowship from “laCaixa” Foundation. Work in the laboratory of M.F.F. was funded by Fundación Científica Asociación Española Contra el Cáncer (AECC) (PROYE18061FER), the Asturias Government (PCTI) co-funding 2018- 2022/FEDER (IDI/2018/146), the Health Institute Carlos III (Plan Nacional de I+D+I) co-funding FEDER (PI18/01527). Work in the laboratory of G.K. was supported by the Ligue contre le Cancer (équipe labellisée); Agence National de la Recherche (ANR)—Projets blancs; ANR under the frame of E-Rare-2, the ERA-Net for Research on Rare Diseases; AMMICa US23/CNRS UMS3655; Association pour la recherche sur le cancer (ARC); Association “Ruban Rose”; Cancéropôle Ile-de-France; Chancelerie des universités de Paris (Legs Poix), Fondation pour la Recherche Médicale (FRM); a donation by Elior; European Research Area Network on Cardiovascular Diseases (ERA-CVD, MINOTAUR); Gustave Roussy Odyssea, the European Union Horizon 2020 Project Oncobiome; Fondation Carrefour; High-end Foreign Expert Program in China (GDW20171100085), Institut National du Cancer (INCa); Inserm (HTE); Institut Universitaire de France; LeDucq Foundation; the LabEx Immuno-Oncology (ANR-18-IDEX-0001); the RHU Torino Lumière; the Seerave Foundation; the SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); and the SIRIC Cancer Research and Personalized Medicine (CARPEM). This study contributes to the IdEx Université de Paris ANR-18-IDEX-0001. Work in the laboratory of W.R. was funded by the Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0425). Work in the laboratory of M.S. was funded by the IRB, and by grants from Spanish Ministry of Economy co-funded by European Regional Development Fund (ERDF) (SAF2013-48256-R), European Research Council (ERC-2014-AdG/669622), Secretaria d'Universitats i Recerca del Departament d'Empresa i Coneixement of Catalonia (Grup de Recerca consolidat 2017 SGR 282) and “laCaixa” Foundation.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices., eLife digest Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels. Traditionally, this involves taking a water sample, followed by growing a few species of ‘indicator bacteria’ that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or ‘sequencing’) the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas. The MinION is a pocket-sized device that – when paired with a laptop or mobile phone – can sequence genetic information ‘on the go’. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction. To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures. For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species – an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality. Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases.

DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets.

BackgroundEpigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data, and which have emerged in the last few years as the most accurate biomarkers of the ageing process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harbouring mutations in proteins of the epigenetic machinery.ResultsUsing the Horvath epigenetic clock, we performed an unbiased screen for epigenetic age acceleration (EAA) in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic ageing. Furthermore, we show that the normal ageing process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterised by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients.ConclusionsThese results suggest that the H3K36 methylation machinery is a key component of theepigenetic maintenance systemin humans, which controls the rate of epigenetic ageing, and this role seems to be conserved in model organisms. Our observations provide novel insights into the mechanisms behind the epigenetic ageing clock and we expect will shed light on the different processes that erode the human epigenetic landscape during ageing.

Here we provide the first genome-wide in vivo analysis of the Na+/Ca2+ exchanger family in the model system Caenorhabditis elegans. We source all members of this family within the Caenorhabditis genus and reconstruct their phylogeny across humans and Drosophila melanogaster. Next, we provide a description of the expression pattern for each exchanger gene in C. elegans, revealing a wide expression in a number of tissues and cell types including sensory neurons, interneurons, motor neurons, muscle cells, and intestinal tissue. Finally, we conduct a series of behavioral and functional analyses through mutant characterization in C. elegans. From these data we demonstrate that, similar to mammalian systems, the expression of Na+/Ca2+ exchangers in C. elegans is skewed toward excitable cells, and we propose that C. elegans may be an ideal model system for the study of Na+/Ca2+ exchangers.