Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method ...for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
Laboratory-based mock crime studies have often been interpreted to mean that (i) eyewitness confidence in an identification made from a lineup is a weak indicator of accuracy and (ii) sequential ...lineups are diagnostically superior to traditional simultaneous lineups. Largely as a result, juries are increasingly encouraged to disregard eyewitness confidence, and up to 30% of law enforcement agencies in the United States have adopted the sequential procedure. We conducted a field study of actual eyewitnesses who were assigned to simultaneous or sequential photo lineups in the Houston Police Department over a 1-y period. Identifications were made using a three-point confidence scale, and a signal detection model was used to analyze and interpret the results. Our findings suggest that (i) confidence in an eyewitness identification from a fair lineup is a highly reliable indicator of accuracy and (ii) if there is any difference in diagnostic accuracy between the two lineup formats, it likely favors the simultaneous procedure.
Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes
. Global ...epigenetic reprogramming accompanies these changes
, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.
The origin of human metaplastic states and their propensity for cancer is poorly understood. Barrett's esophagus is a common metaplastic condition that increases the risk for esophageal ...adenocarcinoma, and its cellular origin is enigmatic. To address this, we harvested tissues spanning the gastroesophageal junction from healthy and diseased donors, including isolation of esophageal submucosal glands. A combination of single-cell transcriptomic profiling, in silico lineage tracing from methylation, open chromatin and somatic mutation analyses, and functional studies in organoid models showed that Barrett's esophagus originates from gastric cardia through c-MYC and HNF4A-driven transcriptional programs. Furthermore, our data indicate that esophageal adenocarcinoma likely arises from undifferentiated Barrett's esophagus cell types even in the absence of a pathologically identifiable metaplastic precursor, illuminating early detection strategies.
Multiple international airway societies have created guidelines for the management of the difficult airway. In critically ill patients, there are physiologic derangements beyond inadequate airway ...protection or hypoxemia. These risk factors contribute to the "physiologically difficult airway" and are associated with complications including cardiac arrest and death. Importantly, they are largely absent from international guidelines. Thus, we created management recommendations for the physiologically difficult airway to provide practical guidance for intubation in the critically ill. Through multiple rounds of in-person and telephone conferences, a multidisciplinary working group of 12 airway specialists (Society for Airway Management's Special Projects Committee) over a time period of 3 years (2016-2019) reviewed airway physiology topics in a modified Delphi fashion. Consensus agreement with the following recommendations among working group members was generally high with 80% of statements showing agreement within a 10% range on a sliding scale from 0% to 100%. We limited the scope of this analysis to reflect the resources and systems of care available to out-of-operating room adult airway providers. These recommendations reflect the practical application of physiologic principles to airway management available during the analysis time period.
Background. The emergence of artemisinin-resistant Plasmodium falciparum in Southeast Asia threatens malaria treatment efficacy. Mutations in a kelch protein encoded on P. falciparum chromosome 13 ...(K13) have been associated with resistance in vitro and in field samples from Cambodia. Methods. P. falciparum infections from artesunate efficacy trials in Bangladesh, Cambodia, Laos, Myanmar, and Vietnam were genotyped at 33 716 genome-wide single-nucleotide polymorphisms (SNPs). Linear mixed models were used to test associations between parasite genotypes and parasite clearance half-lives following artesunate treatment. K13 mutations were tested for association with artemisinin resistance, and extended haplotypes on chromosome 13 were examined to determine whether mutations arose focally and spread or whether they emerged independently. Results. The presence of nonreference K13 alleles was associated with prolonged parasite clearance half-life (P= 1.97 × 10⁻¹²). Parasites with a mutation in any of the K13 kelch domains displayed longer parasite clearance half-lives than parasites with wild-type alleles. Haplotype analysis revealed both population-specific emergence of mutations and independent emergence of the same mutation in different geographic areas. Conclusions. K13 appears to be a major determinant of artemisinin resistance throughout Southeast Asia. While we found some evidence of spreading resistance, there was no evidence of resistance moving westward from Cambodia into Myanmar.
Elucidating genetic causes of cholestasis has proved to be important in understanding the physiology and pathophysiology of the liver. Here we show that protein-truncating mutations in the tight ...junction protein 2 gene (TJP2) cause failure of protein localization and disruption of tight-junction structure, leading to severe cholestatic liver disease. These findings contrast with those in the embryonic-lethal knockout mouse, highlighting differences in redundancy in junctional complexes between organs and species.
Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by ...TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup.
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•An enhanced bisulfite strategy allows genome-wide methylation profiling of zygotes•Gene bodies constitute a major target of zygotic demethylation and TET3 oxidation•The impact of TET3 loss is moderate and implicates redundant demethylation pathways•Protective TET3 activity shields certain CpG islands against methylation buildup
Peat et al. employ whole-genome bisulfite sequencing to generate a global picture of the profound DNA methylation reprogramming that is triggered by fertilization. This identifies gene bodies as a major demethylation target where TET3 oxidation plays an important role and uncovers a protective TET3 function as well as redundancy in the demethylation machinery.
Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and ...embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood.
Here we report a single-cell transcriptomic atlas from Dnmt and Tet mutant mouse embryos during early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos.
This study provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at a whole organism scale and affords new insights into the regulatory mechanisms of cell fate decisions.
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