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Epigenetic regulatory mechanisms are underappreciated, yet are critical for enteric nervous system (ENS) development and maintenance. We discovered that fetal loss of the epigenetic regulator Bap1 in the ENS lineage caused severe postnatal bowel dysfunction and early death in Tyrosinase-Cre [Bap1.sup.fl/fl] mice. Bap1- depleted ENS appeared normal in neonates; however, by P15, Bap1-deficient enteric neurons were largely absent from the small and large intestine of Tyrosinase-Cre [Bap.sup.1fl/fl] mice. Bowel motility became markedly abnormal with disproportionate loss of cholinergic neurons. Single-cell RNA sequencing at P5 showed that fetal Bap1 loss in Tyrosinase-Cre [Bap1.sup.fl/fl] mice markedly altered the composition and relative proportions of enteric neuron subtypes. In contrast, postnatal deletion of Bap1 did not cause enteric neuron loss or impaired bowel motility. These findings suggest that BAP1 is critical for postnatal enteric neuron differentiation and for early enteric neuron survival, a finding that may be relevant to the recently described human BAP1-associated neurodevelopmental disorder., Introduction The enteric nervous system (ENS) rivals the spinal cord in complexity, with more than 20 neuron and at least 4 glial subtypes forming integrated circuits throughout the bowel (1, [...]

Rana sylvatica (also known as Boreorana sylvatica) is one of the few vertebrates that spend extreme winters showing no physiological signs of life. Up to 70% of the total body water of the wood frog freezes as extracellular ice. Survival in extreme conditions requires regulation at transcriptional and translational levels to activate prosurvival pathways. N6-methyladenosine ([m.sup.6]A) methylation is one of the most common RNA modifications, regulating transcript processing and translation by executing important functions that affect regulatory pathways in stress conditions. In the study, regulation of [m.sup.6]A-related proteins in the liver of R. sylvatica was analyzed during 24 h frozen and 8 h thaw conditions. Decreases in the activity of demethylases of 28.44 [+ or -] 0.4% and 24.1 [+ or -] 0.9% of control values in frozen and thaw tissues, respectively, were observed. Total protein levels of [m.sup.6]A methyltransferase complex components methyltransferase-like 14 and Wilm's tumor associated protein were increased by 1.28-fold and 1.42-fold, respectively, during freezing. Demethylase fat mass and obesity, however, showed a decreasing trend, with a significant decrease in abundance during recovery from frozen conditions. Levels of mRNA degraders YTHDF2 and YTHDC2 also decreased under stress. Overall, increased levels of [m.sup.6]A methylation complex components, and suppressed levels of readers/erasers, provide evidence for the potential role of RNA methylation in freezing survival and its regulation in a hypometabolic state. Key words: epigenetics, freeze tolerance, RNA methylation, metabolic rate depression, Rana sylvatica (Boreorana sylvatica), Introduction The wood frog, Rana sylvatica (Boreorana sylvatica), is one of the freeze-tolerant model organisms that survive sub-zero temperatures for several months. During freezing, the wood frog employs multiple adaptation [...]

About 25% of people in the general population are insulin resistant, increasing the risk for type 2 diabetes (T2D) and metabolic disease. Transcriptomic analysis of induced pluripotent stem cells differentiated into myoblasts (iMyos) from insulin-resistant (I-Res) versus insulin-sensitive (I-Sen) nondiabetic individuals revealed that 306 genes increased and 271 genes decreased in expression in iMyos from I-Res donors with differences of 2- fold or more. Over 30 of the genes changed in I-Res iMyos were associated with T2D by SNPs and were functionally linked to insulin action and control of metabolism. Interestingly, we also identified more than 1,500 differences in gene expression that were dependent on the sex of the cell donor, some of which modified the insulin resistance effects. Many of these sex differences were associated with increased DNA methylation in cells from female donors and were reversed by 5-azacytidine. By contrast, the insulin sensitivity differences were not reversed and thus appear to reflect genetic or methylation- independent epigenetic effects., Introduction Insulin resistance underlies the development of type 2 diabetes (T2D) and metabolic syndrome (1-3), which together affect 20%-30% of adults in Westernized populations (4). In addition, an almost equal [...]

Cutting-edge DNA methylation-based epigenetic aging techniques were applied to Gulf of Mexico northern red snapper (Lutjanus campechanus; n = 10; 1-26 years old) and red grouper (Epinephelus morio; n = 10; 2-14 years old). Bisulfiteconverted restriction site-associated DNA sequencing was used to identify CpG sites (cytosines followed by guanines) that exhibit age-correlated DNA methylation, and species-specific epigenetic clocks developed from hundreds of CpG sites in each species showed strong agreement between predicted and otolith-derived age [r.sup.2] > 0.99 for both species). Results suggest epigenetic age estimation could provide an accurate and efficient approach to mass-aging fishes in a non-invasive manner. Des methodes epigenetiques de pointe de determination de l'age reposant sur la methylation de l'ADN ont ete appliquees au vivaneau campeche (Lutjanus campechanus; n = 10; 1-26 ans) et au merou rouge (Epinephelus morio; n = 10; 2-14 ans). Le sequencage avec conversion au bisulfite d'ADN associe a des sites de restriction a ete utilise pour cerner des sites CpG (cytosines suivies de guanines) qui presentent une methylation de l'ADN correlee a l'age, et des horloges epigenetiques propres a l'espece developpees a partir de centaines de sites CpG de chaque espece ont revele de fortes concordances entre les ages predits et les ages obtenus par analyse d'otolites [r.sup.2] > 0,99 pour les deux especes). Les resultats donnent a penser que l'estimation epigenetique de l'age pourrait constituer une approche non invasive exacte et efficiente de determination des ages de quantites massives de poissons., Introduction Age data are fundamental to determining life history parameters (e.g., age-at-length, age-at-maturity, age-related fecundity) and are thus critical for fisheries assessment and management, particularly when age-structured stock assessment models [...]

Author(s): Michael Song [sup.1] [sup.2] , Mark-Phillip Pebworth [sup.3] [sup.4] , Xiaoyu Yang [sup.1] , Armen Abnousi [sup.5] , Changxu Fan [sup.6] [sup.7] , Jia Wen [sup.8] , Jonathan D. [...], Lineage-specific epigenomic changes during human corticogenesis have been difficult to study owing to challenges with sample availability and tissue heterogeneity. For example, previous studies using single-cell RNA sequencing identified at least 9 major cell types and up to 26 distinct subtypes in the dorsal cortex alone.sup.1,2. Here we characterize cell-type-specific cis-regulatory chromatin interactions, open chromatin peaks, and transcriptomes for radial glia, intermediate progenitor cells, excitatory neurons, and interneurons isolated from mid-gestational samples of the human cortex. We show that chromatin interactions underlie several aspects of gene regulation, with transposable elements and disease-associated variants enriched at distal interacting regions in a cell-type-specific manner. In addition, promoters with increased levels of chromatin interactivity--termed super-interactive promoters--are enriched for lineage-specific genes, suggesting that interactions at these loci contribute to the fine-tuning of transcription. Finally, we develop CRISPRview, a technique that integrates immunostaining, CRISPR interference, RNAscope, and image analysis to validate cell-type-specific cis-regulatory elements in heterogeneous populations of primary cells. Our findings provide insights into cell-type-specific gene expression patterns in the developing human cortex and advance our understanding of gene regulation and lineage specification during this crucial developmental window. Analysis of cis-regulatory chromatin interactions, open chromatin and transcriptomes for different cell types isolated from mid-gestational human cortex samples provides insights into gene regulation during development.

Author(s): Zheng Li [sup.1] , Shuai Zhao [sup.2] , Raman V. Nelakanti [sup.1] , Kaixuan Lin [sup.1] , Tao P. Wu [sup.1] [sup.7] , Myles H. Alderman III [sup.1] , [...], The recent discovery of N.sup.6-methyladenine (N.sup.6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism.sup.1. However, the biological role of N.sup.6-mA and the molecular pathways that exert its function remain unclear. Here we show that N.sup.6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N.sup.6-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD).sup.2-4. Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures.sup.3,5,6. We show that the presence of N.sup.6-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N.sup.6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N.sup.6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD-SATB1 interactions mediated by N.sup.6-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N.sup.6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development. The DNA modification N.sup.6-methyladenine regulates gene expression during mouse trophoblast development by depositing at the boundaries of active chromatin and preventing its spread by antagonizing the chromatin organizer SATB1.