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5-methylcytosine is a major epigenetic modification that is sometimes called “the fifth nucleotide.” However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes, including zebrafish gametes and early embryos. The oocyte methylome is significantly hypomethylated compared to sperm. Strikingly, the paternal DNA methylation...
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the authors.In this article, we claimed that Angptl-8, which we termed betatrophin and is also referred to in the literature as TD26, RIFL, C19orf80, and Lipasin, was the agent by which the insulin antagonist S961 induces...
Daily metabolic patterns are regulated in a circadian manner often via the hypothalamic axis. Mukherji et al. now report a surprising role for commensal bacteria in the circadian regulation of glucocorticoid production by intestinal epithelial cells.
Defining determinants of T cell fate is central to understanding adaptive immunity and the design of effective vaccines. Tubo et al. demonstrate that intrinsic properties of T cell receptor signaling dictate whether CD4 T cells adopt predominantly type 1 helper or follicular helper T cell phenotypes in response to bacterial or viral infection.
RNAP II is frequently paused near gene promoters in mammals, and its transition to productive elongation requires active recruitment of P-TEFb, a cyclin-dependent kinase for RNAP II and other key transcription elongation factors. A fraction of P-TEFb is sequestered in an inhibitory complex containing the 7SK noncoding RNA, but it has been unclear how P-TEFb is switched from the 7SK complex to RNAP...
Alterations of symbiosis between microbiota and intestinal epithelial cells (IEC) are associated with intestinal and systemic pathologies. Interactions between bacterial products (MAMPs) and Toll-like receptors (TLRs) are known to be mandatory for IEC homeostasis, but how TLRs may time homeostatic functions with circadian changes is unknown. Our functional and molecular dissections of the IEC circadian...
All metazoan guts are subjected to immunologically unique conditions in which an efficient antimicrobial system operates to eliminate pathogens while tolerating symbiotic commensal microbiota. However, the molecular mechanisms controlling this process are only partially understood. Here, we show that bacterial-derived uracil acts as a ligand for dual oxidase (DUOX)-dependent reactive oxygen species...
Strategies in life science graduate education must evolve in order to train a modern workforce capable of integrative solutions to challenging problems. Our institution has catalyzed such evolution through building a postdoctoral Curriculum Fellows Program that provides a collaborative and scholarly education laboratory for innovation in graduate training.
In this issue of Cell, Loffredo et al. demonstrate that exposing an old mouse to the circulatory system of a young mouse reverses age-related cardiac hypertrophy. The authors demonstrate that this effect can be recapitulated by treating old mice with growth and differentiation factor 11 (GDF11). These data suggest that GDF11 therapy may be a useful tool in combating age-related cardiac hypertrophy.
A naive CD4+ T cell population specific for a microbial peptide:major histocompatibility complex II ligand (p:MHCII) typically consists of about 100 cells, each with a different T cell receptor (TCR). Following infection, this population produces a consistent ratio of effector cells that activate microbicidal functions of macrophages or help B cells make antibodies. We studied the mechanism that underlies...
Mice carrying mutations in multiple genes are traditionally generated by sequential recombination in embryonic stem cells and/or time-consuming intercrossing of mice with a single mutation. The CRISPR/Cas system has been adapted as an efficient gene-targeting technology with the potential for multiplexed genome editing. We demonstrate that CRISPR/Cas-mediated gene editing allows the simultaneous disruption...
Visualization of living E. coli nucleoids, defined by HupA-mCherry, reveals a discrete, dynamic helical ellipsoid. Three basic features emerge. (1) Nucleoid density coalesces into longitudinal bundles, giving a stiff, low-DNA-density ellipsoid. (2) This ellipsoid is radially confined within the cell cylinder. Radial confinement gives helical shape and directs global nucleoid dynamics, including sister...
Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation (ZGA). To understand this process, we determined the DNA methylation (DNAme) profiles of zebrafish gametes, embryos at different stages, and somatic muscle and compared them to gene activity and histone modifications. Sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly, the DNA of...
Identification of somatic rearrangements in cancer genomes has accelerated through analysis of high-throughput sequencing data. However, characterization of complex structural alterations and their underlying mechanisms remains inadequate. Here, applying an algorithm to predict structural variations from short reads, we report a comprehensive catalog of somatic structural variations and the mechanisms...
Sexual dimorphisms in the brain underlie behavioral sex differences, but the function of individual sexually dimorphic neuronal populations is poorly understood. Neuronal sexual dimorphisms typically represent quantitative differences in cell number, gene expression, or other features, and it is unknown whether these dimorphisms control sex-typical behavior exclusively in one sex or in both sexes...
Epigenetic reprogramming of parental genomes following fertilization is important to ensure compatibility for totipotency and development thereafter. New studies by Jiang et al. and Potok et al. now demonstrate how the parental DNA methylomes are reset in zebrafish and reveal striking differences from events in mammals.
Tumor necrosis factor-α (TNF-α) is the most potent proinflammatory cytokine in mammals. The degradation of TNF-α mRNA is critical for restricting TNF-α synthesis and involves a constitutive decay element (CDE) in the 3′ UTR of the mRNA. Here, we demonstrate that the CDE folds into an RNA stem-loop motif that is specifically recognized by Roquin and Roquin2. Binding of Roquin initiates degradation...
Viruses are a widespread persistent threat to human health, and for the most dangerous threats, effective antiviral therapies or vaccines are often still lacking. To combat the rapid pace of viral evolution and the continual emergence of new strains, broadly neutralizing therapies or vaccines that can target multiple strains are in high demand. In this Select, we look at recent papers that are helping...
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