Hepatic ontogeny and tissue distribution of mRNAs of epigenetic modifiers in mice using RNA-sequencing

Developmental regulation of gene expression is controlled by distinct epigenetic signatures catalyzed by various epigenetic modifiers. Little is known about the ontogeny and tissue distribution of these epigenetic modifiers. In the present study, we used a novel approach of RNA-sequencing to elucidate hepatic ontogeny and tissue distribution of mRNA expression of 142 epigenetic modifiers, including enzymes involved in DNA methylation/demethylation, histone acetylation/deacetylation, histone methylation/demethylation, histone phosphorylation and chromosome remodeling factors in male C57BL/6 mice. Livers from male C57BL/6 mice were collected at 12 ages from prenatal to adulthood. Many of these epigenetic modifiers were expressed at much higher levels in perinatal livers than adult livers, such as Dnmt1, Dnmt3a, Dnmt3b, Apobec3, Kat1, Ncoa4, Setd8, Ash2l, Dot1l, Cbx1, Cbx3, Cbx5, Cbx6, Ezh2, Suz12, Eed, Suv39h1, Suv420h2, Dek, Hdac1, Hdac2, Hdac7, Kdm2b, Kdm5c, Kdm7, Prmt1–5, Prmt7, Smarca4, Smarcb1, Chd4 and Ino80e. In contrast, hepatic mRNA expression of a few epigenetic modifiers increased during postnatal liver development, such as Smarca2, Kdm1b, Cbx7 and Chd3. In adult mice (60 d of age), most epigenetic modifiers were expressed at moderately (1–3-fold) higher levels in kidney and/or small intestine than liver. In conclusion, this study, for the first time, unveils developmental changes in mRNA abundance of all major known epigenetic modifiers in mouse liver. These data suggest that ontogenic changes in mRNA expression of epigenetic modifiers may play important roles in determining the addition and/or removal of corresponding epigenetic signatures during liver development.     

共培养对小鼠囊胚质量及其表观遗传修饰的影响

本研究探讨了共培养对小鼠囊胚质量及其表观遗传修饰的影响。将小鼠的受精卵体外随机分别置于含颗粒细胞(试验组I)、输卵管上皮细胞(试验组Ⅱ)、输卵管组织块(试验组Ⅲ)的KSOM培养液中作为试验组进行共培养,同时设立对照组A(体外培养,仅含KSOM)和对照组B(体内培养)。比较各组受精卵的卵裂率和囊胚发育率;并应用碘化丙啶和Hoechest333258对囊胚进行染色,利用ICM/TE值评价各组胚胎体外发育的质量;同时将囊胚进行免疫荧光染色,观察其基因组甲基化和组蛋白乙酰化的水平。结果表明,与对照组A相比,试验组的卵裂率和囊胚发育率均有显著提高(P<0.05);同时其囊胚细胞数目及内细胞团细胞数与滋养层细胞数比值(ICM/TE)值均显著高于对照组A(P<0.05);各试验组囊胚基因组甲基化水平与对照组A差异不显著(P>0.05),但各体外培养组均与对照组B差异显著(P<0.05);试验组组蛋白乙酰化水平与对照组A、B差异均不显著(P>0.05)。共培养能够有效促进小鼠胚胎的体外发育,提高囊胚的发育质量,但是仍不能克服由体外培养造成的基因组甲基化异常。     

Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice

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Aminopeptidase N during the ontogeny of the chick

Little is known about the production and function of metallopeptidases in embryonic development. One such enzyme, aminopeptidase N (APN), is present in several epithelia, the brain and angiogenic vessels in adults. APN promotes vascular growth and endothelial cell proliferation in physiological and pathological models of angiogenesis. However, its possible role in embryonic angiogenesis or other developmental processes is unknown. Its expression profile in the early phase of embryonic development has not been reported. We report here the expression of this enzyme during the early development of the chick embryo, using complementary techniques for monitoring APN mRNA, protein, and enzymatic activity. We detected APN in the embryo as early as gastrulation. In addition to the known sites of APN production identified in both adults and rat fetuses toward the end of gestation, APN was found in unexpected sites, such as the primitive streak, the dorsal folds of the neural tube, the somites, and the primordia of several organs. APN was present mostly in the cardiovascular compartment during the first 13 days of incubation, and in the hematopoietic compartment (yolk sac and aorta-gonad-mesonephros region) early in development. This study provides clues as to the possible role of APN in embryonic development.     

Effect of zinc supplementation on metallothionein,copper, and zinc concentration in various tissues of copper-loaded rats

The present study was designed to investigate the effects of Zn administration on metallothionein concentrations in the liver, kidney, and intestine of copper-loaded rats. Male CD rats were fed a diet containing 12 mg Cu and 67 mg Zn/kg body wt. They were divided into either acute or chronic experimental protocols. Rats undergoing acute experiments received daily ip injections of either Cu (3 mg/kg body wt) or Zn (10 mg/kg body wt) for 3 d. Chronic experiments were carried out on rats receiving Cu ip injections on d 1, 2, 3, 10, 17, and 24, Cu injections plus a Zn-supplemented diet containing 5 g Zn/kg solid diet, or a Zn-supplemented diet alone. Rats injected Zn or Cu had increased MT concentrations in liver and kidney. Zn produced the most important effects and the liver was the most responsive organ. Rats fed a Zn-supplemented diet had significantly higher MT concentrations in liver and intestine with respect to controls. Increased MT synthesis in the liver may contribute to copper detoxification; the hypothesis of copper entrapment in enterocytes cannot be confirmed.     

利用RNA-seq技术分析淹水胁迫下转BnERF拟南芥差异表达基因

为探究淹水胁迫下BnERF调节的耐淹防御相关途径,应用RNA-seq技术,对淹水6小时后的拟南芥(Arabidopsis thaliana)野生型(WT)和转BnERF株系(E33)幼苗进行基因表达分析。结果表明,淹水3天后,E33表现出较强的耐淹性,地上部生长状况和根系发育均明显强于野生型。E33幼苗未淹水处理时相对于野生型单独上调的基因有9个,4个为膜结合蛋白,其中2个参与MAPK级联途径,其它5个参与氧化胁迫及水分调节途径;与未淹水野生型相比,无论是未淹水处理还是淹水6小时后的E33幼苗中缺氧响应、抗氧化防护及细胞、器官发育相关基因的表达量均上调。另外,淹水6小时后E33的差异基因并未完全覆盖淹水6小时后野生型的差异基因;E33幼苗中缺氧响应、氧化胁迫响应、能量的产生与转变、乙醇代谢途径中的基因以及乙烯响应因子基因的表达量都明显高于野生型。上述结果表明,BnERF直接或间接调节植物的淹水胁迫相关生理代谢途径,参与淹水胁迫的防御过程。     

Ontogeny of the cell adhesion molecule L1 in the cerebellum of weaver and reeler mutant mice

The ontogeny of cell adhesion molecule L1 in cerebellum was quantitatively assessed in weaver and reeler mutant mice and in heterozygous litter-mate controls. In the latter the concentration and the amount of L1 both increased from the first postnatal week to become maximum at the second. In contrast, in the weaver and reeler neurologic mutant mice, L1 decreased steadily. The L1 concentration and the amount of L1 was lower in the cerebellum of homozygous mutant mice than in litter-mate controls. The findings are consistent with L1 being a component of axonal plasma membranes. However, no evidence was found of any direct effect of thewv andrl phenotypes on L1 expression.     

表观遗传生物标志物在人类疾病早期诊治中的研究进展

表观遗传修饰异常见于人类的多种疾病(如肿瘤、老年性疾病、发育源性疾病等),影响着这些疾病的发生发展。已有的研究表明,异常表观遗传改变可以作为疾病状态和疾病预测的生物标志物。表观遗传修饰改变的可逆性和可控性也为疾病早期的预防和治疗提供了新策略。本文对DNA甲基化修饰、组蛋白共价修饰、非编码RNA等三种表观遗传方式在肿瘤、老年性疾病和发育源性疾病的研究,以及三者作为表遗传生物标志物在疾病早期诊断和治疗的应用展开介绍,以期为肿瘤、老年性和发育源性相关疾病的诊断与治疗提供借鉴和 参考。     

Genetic modifiers of the Kv beta2-null phenotype in mice

Shaker-type potassium (K+) channels are composed of pore-forming alpha subunits associated with cytoplasmic beta subunits. Kv beta2 is the predominant Kv beta subunit in the mammalian nervous system, but its functions in vivo are not clear. Kv beta2-null mice have been previously characterized in our laboratory as having reduced lifespans, cold swim-induced tremors and occasional seizures, but no apparent defect in Kv alpha-subunit trafficking. To test whether strain differences might influence the severity of this phenotype, we analyzed Kv beta2-null mice in different strain backgrounds: 129/SvEv (129), C57BL/6J (B6) and two mixed B6/129 backgrounds. We found that strain differences significantly affected survival, body weight and thermoregulation in Kv beta2-null mice. B6 nulls had a more severe phenotype than 129 nulls in these measures; this dramatic difference did not reflect alterations in seizure thresholds but may relate to strain differences we observed in cerebellar Kv1.2 expression. To specifically test whether Kv beta1 is a genetic modifier of the Kv beta2-null phenotype, we generated Kv beta1.1-deficient mice by gene targeting and bred them to Kv beta2-null mice. Kv beta1.1/Kv beta2 double knockouts had significantly increased mortality compared with either single knockout but still maintained surface expression of Kv1.2, indicating that trafficking of this alpha subunit does not require either Kv beta subunit. Our results suggest that genetic differences between 129/SvEv and C57Bl/6J are key determinants of the severity of defects seen in Kv beta2-null mice and that Kv beta1.1 is a specific although not strain-dependent modifier.     

The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

The degree to which the ontogeny of organisms could facilitate our understanding of phylogenetic relationships has long been a subject of contention in evolutionary biology. The famed notion that ‘ontogeny recapitulates phylogeny’ has been largely discredited, but there remains an expectation that closely related organisms undergo similar morphological transformations throughout ontogeny. To test this assumption, we used three‐dimensional geometric morphometric methods to characterize the cranial morphology of 10 extant crocodylian species and construct allometric trajectories that model the post‐natal ontogenetic shape changes. Using time‐calibrated molecular and morphological trees, we employed a suite of comparative phylogenetic methods to assess the extent of phylogenetic signal in these trajectories. All analyses largely demonstrated a lack of significant phylogenetic signal, indicating that ontogenetic shape changes contain little phylogenetic information. Notably, some Mantel tests yielded marginally significant results when analysed with the morphological tree, which suggest that the underlying signal in these trajectories is correlated with similarities in the adult cranial morphology. However, despite these instances, all other analyses, including more powerful tests for phylogenetic signal, recovered statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness and thus bring into question the efficacy of using allometric trajectories for phylogenetic inference.     

The ontogeny and cost of migration in Drosophila subobscura Collin

The ontogeny of migratory potential of male and female Drosophila subobscura has been quantified using tethered flight in the laboratory. In both sexes there is an increase in the few days immediately after eclosion, and a decline before the flies cease reproductive activity. There is an intervening peak in the potential of males, which may result from an increased rejection-rate by inseminated females. The migratory potential generally appears greater than that usually utilized in the field. Such extended migration extracts a significant cost from female flies in terms of reduced fecundity.     

Lateral asymmetry of kidney weights in different populations of wild mice

Weights of right and left kidneys were compared in different populations of wild mice. Samples were taken from Great Britain, Pacific islands and Sub-Antarctica. The different population samples were further subdivided according to sex and age as estimated by tooth category (i.e., degree of development or wear of upper molars). The mean weights of right kidneys exceeded those on the left in all 28 Subsamples but the data suggested mat this difference decreased with age. The evidence further suggested that the asymmetry between the two kidneys was greater in populations of small mice from the Pacific islands than in those of large mice from Britain and Sub-Antarctica. On the basis of published data on rats and guinea pigs the question is raised whether interspecific differences in kidney asymmetry may be explicable by differences in the sizes of the kidneys in different species.     

The penetrance of an epigenetic trait in mice is progressively yet reversibly increased by selection and environment

Natural selection acts on variation that is typically assumed to be genetic in origin. But epigenetic mechanisms, which are interposed between the genome and its environment, can create diversity independently of genetic variation. Epigenetic states can respond to environmental cues, and can be heritable, thus providing a means by which environmentally responsive phenotypes might be selectable independent of genotype. Here, we have tested the possibility that environment and selection can act together to increase the penetrance of an epigenetically determined phenotype. We used isogenic A(vy) mice, in which the epigenetic state of the A(vy) allele is sensitive to dietary methyl donors. By combining methyl donor supplementation with selection for a silent A(vy) allele, we progressively increased the prevalence of the associated phenotype in the population over five generations. After withdrawal of the dietary supplement, the shift persisted for one generation but was lost in subsequent generations. Our data provide the first demonstration that selection for a purely epigenetic trait can result in cumulative germline effects in mammals. These results present an alternative to the paradigm that natural selection acts only on genetic variation, and suggest that epigenetic changes could underlie rapid adaptation of species in response to natural environmental fluctuations.     

Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice

Intrauterine nutrition can program metabolism, creating stable changes in physiology that may have significant health consequences. The mechanism underlying these changes is widely assumed to involve epigenetic changes to the expression of metabolic genes, but evidence supporting this idea is limited. Here we have performed the first study of the epigenomic consequences of exposure to maternal obesity and diabetes. We used a mouse model of natural-onset obesity that allows comparison of genetically identical mice whose mothers were either obese and diabetic or lean with a normal metabolism. We find that the offspring of obese mothers have a latent metabolic phenotype that is unmasked by exposure to a Western-style diet, resulting in glucose intolerance, insulin resistance and hepatic steatosis. The offspring show changes in hepatic gene expression and widespread but subtle alterations in cytosine methylation. Contrary to expectation, these molecular changes do not point to metabolic pathways but instead reside in broadly developmental ontologies. We propose that, rather than being adaptive, these changes may simply produce an inappropriate response to suboptimal environments; maladaptive phenotypes may be avoidable if postnatal nutrition is carefully controlled.     

Constraints in the ligament ontogeny and evolution of pteriomorphian Bivalvia

A study of ligaments of larval, postlarval and adult shells of fossil and recent pteriomorphian bivalves leads to the following observations and hypotheses: (1) Ligament growth passively follows the general growth pattern of the mantle margin. No independent genetic information fixes the anterior, ventral, or posterior growth direction of the ligament. Further growth constraints relate to physical availability of space on the ligament area and to heterochronic processes. (2) The disjunct ligament and the repetition of fibrous or lamellar sublayers are phenotypic aspects of the same derived ligament Bauplan 1. All Pteriomorphia possess the ability to produce repetitive ligaments. This ability and space reductions of the ligament area in independent phylogenetic lineages are responsible for the iterative evolution of ligament grades. (3) Spondylidae and Plicatulidae are duplivincular, and the Ostreoidea are plesiomorphically multivincular. (4) Larval anterior-helical growth of the soft tissue produces opisthogyrate shells and possibly caused the evolution of the alivincular-multivincular grade. Duplivincular-alivincular and multivincular-alivincular grades can be distinguished if larval shell characters are known. (5) The taxonomic distribution of ligament grades as amended in this paper is largely consistent with modern phylogeny hypotheses based on genetic or morphologic or combined character sets. However, the resolution of early phylogenetic nodes requires more data on larval shells of Lower Palaeozoic taxa.