Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model

Sex-specific effects of a methionine-restricted maternal diet on liver transcript levels and fatty liver production in mule ducks

Sex-specific effects of maternal diet on offspring phenotypes have been reported in farm animals including in poultry. The present study was conducted in mule ducks, investigating the long-term effects of a methionine-restricted maternal diet on the production performance of the offspring of both sexes. Sixty female ducks were divided into two groups and fed either a control diet containing 4.0 g/kg of methionine or a restricted diet containing 2.5 g/kg of methionine. Next, 254 offspring were divided into four subgroups of 60-67 animals, according to maternal diet and sex. Their growth performance was recorded until 87 days of age. Then, plasma parameters were measured on these non-overfed ducks (NOFDs) at D87 and 60 of them were sacrificed, representing 15 males and 15 females in each maternal diet group. Carcass traits were recorded, and the liver transcript level of 170 genes mainly involved in energy or one-carbon metabolism was studied. The remaining 194 ducks were overfed during 12.5 days -until 100 days of age- for fatty liver production. Then, zootechnical traits and plasma parameters were measured on these 194 overfed ducks (OFDs), and the liver transcript level of the same 170 genes was studied. The results showed that the methionine-restricted maternal diet affected traits in NOFDs but in females only, with lower liver lipid and DM percentages (P-value = 0.006 and P-value = 0.004, respectively) and a lower plasma cholesterol level (P-value = 0.020). In OFDs, after the overfeeding period, fatty liver weight was reduced in both sexes by around 53 g, or almost 10% (P-value = 0.016 and 0.017 in females and males, respectively). Only females showed a tendency to lower liver lipid and DM percentages (P-value = 0.078 and P-value = 0.062, respectively) and their plasmatic aspartate aminotransferase activity was reduced (P-value = 0.025). In addition, 18 genes differentially expressed between maternal diet groups were identified in the liver of females only. All were up-regulated in the restricted group and involved in either energy or one-carbon metabolism. These findings showed that the methionine-restricted maternal diet had long-term effects on liver traits, impacting production performance in both sexes. Importantly, these effects were sex-specific, and robust enough to still be observed after the overfeeding period, despite the major reorganisation of metabolic pathways this implied.

Epigenetic programming of chicken germ cells: a comparative review

Chicken embryos serve as an important model for investigating germ cells due to their ease of accessibility and manipulation within the egg. Understanding the development of germ cells is particularly crucial, as they are the only cell types capable of transmitting genetic information to the next generation. Therefore, gene expression regulation in germ cells is important for genomic function. Epigenetic programming is a crucial biological process for the regulation of gene expression without altering the genome sequence. Although epigenetic programming is evolutionarily conserved, several differences between chickens and mammals have been revealed. In this review, we compared the epigenetic regulation of germ cells in chickens and mammals (mainly mice as a representative species). In mammals, migrating primordial germ cells (precursors for germ cells [PGCs]) undergo global DNA demethylation and persist until sexual differentiation, while in chickens, DNA is demethylated until reaching the gonad but remethylated when sexually differentiated. Prospermatogonia is methylated at the onset of mitotic arrest in mammals, while DNA is demethylated at mitotic arrest in chickens. Furthermore, genomic imprinting and inactivation of sex chromosomes are differentially regulated through DNA methylation in chickens and mammals. Chickens and mammals exhibit different patterns of histone modifications during germ cell development, and non-coding RNA, which is not involved in PGC differentiation in mice, plays an important role in chicken PGC development. Additionally, several chicken-specific non-coding RNAs have been identified. In conclusion, we summarized current knowledge of epigenetic gene regulation of chicken germ cells, comparing that of mammals, and highlighted notable differences between them.

Maternal dietary methionine restriction alters the expression of energy metabolism genes in the duckling liver

Background

In mammals, the nutritional status experienced during embryonic development shapes key metabolic pathways and influences the health and phenotype of the future individual, a phenomenon known as nutritional programming. In farmed birds as well, the quantity and quality of feed offered to the dam can impact the phenotype of the offspring. We have previously reported that a 38% reduction in the intake of the methyl donor methionine in the diet of 30 female ducks during the growing and laying periods - from 10 to 51 weeks of age - reduced the body weight of their 180 mule ducklings compared to that of 190 ducklings from 30 control females. The maternal dietary methionine restriction also altered the hepatic energy metabolism studied in 30 of their ducklings. Thus, their plasma glucose and triglyceride concentrations were higher while their plasma free fatty acid level was lower than those measured in the plasma of 30 ducklings from the control group. The objective of this new study was to better understand how maternal dietary methionine restriction affected the livers of their newly hatched male and female ducklings by investigating the hepatic expression levels of 100 genes primarily targeting energy metabolism, amino acid transport, oxidative stress, apoptotic activity and susceptibility to liver injury.

Results

Sixteen of the genes studied were differentially expressed between the ducklings from the two groups. Maternal dietary methionine restriction affected the mRNA levels of genes involved in different pathways related to energy metabolism such as glycolysis, lipogenesis or electron transport. Moreover, the mRNA levels of the nuclear receptors PPARGC1B, PPARG and RXRA were also affected.

Conclusions

Our results show that the 38% reduction in methionine intake in the diet of female ducks during the growing and egg-laying periods impacted the liver transcriptome of their offspring, which may explain the previously observed differences in their liver energy metabolism. These changes in mRNA levels, together with the observed phenotypic data, suggest an early modulation in the establishment of metabolic pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08634-1.

Differential Methylation and Transcriptome Integration Analysis Identified Differential Methylation Annotation Genes and Functional Research Related to Hair Follicle Development in Sheep

Hair follicle growth and development are a complex and long-term physiological process, which is regulated by a variety of physical factors and signal pathways. Increasing the understanding of the epigenetic regulation and function of candidate genes related to hair follicle development will help to better understand the molecular regulatory mechanisms of hair follicle development. In this study, the methylated DNA immunoprecipitation sequencing (MeDIP-seq) was used to obtain the genome-wide methylation map of the hair follicular development of Super Merino sheep in six stages (fetal skin tissue at 65d, 85d, 105d, 135d, 7d, and 30d after birth). Combined with the results of previous RNA-sequencing, 65 genes were screened out that were both differential methylation and differential expression, including EDN1, LAMC2, NR1D1, RORB, MyOZ3, and WNT2 gene. Differential methylation genes were enriched in Wnt, TNF, TGF-beta, and other signaling pathways related to hair follicle development. The bisulfite sequencing PCR results and MeDIP-seq were basically consistent, indicating that the sequencing results were accurate. As a key gene in the Wnt signaling pathway, both differential methylation and expression gene identified by MeDIP-seq and RNA-seq, further exploration of the function of WNT2 gene revealed that the DNA methylation of exon 5 (CpG11 site) promoted the expression of WNT2 gene. The overexpression vector of lentivirus pLEX-MCS-WNT2 was constructed, and WNT2 gene effectively promoted the proliferation of sheep skin fibroblasts. The results showed that WNT2 gene could promote the growth and development of skin and hair follicles. The results of this study will provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.

Chicken embryo as a model in epigenetic research

Epigenetics is defined as the study of changes in gene function that are mitotically or meiotically heritable and do not lead to a change in DNA sequence. Epigenetic modifications are important mechanisms that fine tune the expression of genes in response to extracellular signals and environmental changes. In vertebrates, crucial epigenetic reprogramming events occur during early embryogenesis and germ cell development. Chicken embryo, which develops external to the mother's body, can be easily manipulated in vivo and in vitro, and hence, it is an excellent model for performing epigenetic studies. Environmental factors such as temperature can affect the development of an embryo into the phenotype of an adult. A better understanding of the environmental impact on embryo development can be achieved by analyzing the direct effects of epigenetic modifications as well as their molecular background and their intergenerational and transgenerational inheritance. In this overview, the current possibility of epigenetic changes during chicken embryonic development and their effects on long-term postembryonic development are discussed.

Effect of contact incubation on stress, behavior and body composition in the precocial Red jungle fowl

Birds use contact incubation to warm their eggs above ambient temperature required for embryonic development. In contrast, birds in the industry as well as many birds in breeding programs and scientific studies are incubated in conventional incubators that warm eggs via circulating warm air. This means that contact incubated eggs have different thermal properties than eggs incubated in a conventional incubator. In light of previous studies showing that small differences in incubation temperature can affect chicks post-hatching phenotype, we investigated the consequences of incubating Red jungle fowl eggs at the same temperature (37 °C) either via contact incubation or warm air incubation. We found that contact incubated chicks had a more robust body composition, were more explorative and had a higher temperature preference early in life, as well as a sex dependent difference in plasma Corticosterone levels pre-hatch (measured in down-feathers) and post-hatch (measured in plasma) compared to chicks incubated in a conventional warm air incubator. While previous studies have demonstrated that embryonic development and post-hatch phenotype is sensitive to small variations in temperature, our study demonstrates for the first time that the way heat is distributed to the egg has a similar magnitude of effect on post-hatch phenotype and highlights the sensitivity of the incubation period in shaping birds post-hatch phenotype.

FifBase: a comprehensive fertility-associated indicators factor database for domestic animals

Fertility refers to the ability of animals to maintain reproductive function and give birth to offspring, which is an important indicator to measure the productivity of animals. Fertility is affected by many factors, among which environmental factors may also play key roles. During the past years, substantial research studies have been conducted to detect the factors related to fecundity, including genetic factors and environmental factors. However, the identified genes associated with fertility from countless previous studies are randomly dispersed in the literature, whereas some other novel fertility-related genes are needed to detect from omics-based datasets. Here, we constructed a fertility index factor database FifBase based on manually curated published literature and RNA-Seq datasets. During the construction of the literature group, we obtained 3301 articles related to fecundity for 13 species from PubMed, involving 2823 genes, which are related to 75 fecundity indicators or 47 environmental factors. Eventually, 1558 genes associated with fertility were filtered in 10 species, of which 1088 and 470 were from RNA-Seq datasets and text mining data, respectively, involving 2910 fertility-gene pairs and 58 fertility-environmental factors. All these data were cataloged into FifBase (http://www.nwsuaflmz.com/FifBase/), where the fertility-related factor information, including gene annotation and environmental factors, can be browsed, retrieved and downloaded with the user-friendly interface.

Effect of dietary N-carbamylglutamate on development of ovarian follicles via enhanced angiogenesis in the chicken

N-carbamylglutamate (NCG), an analogue of N-acetyl-L-glutamate (NAG), can increase arginine synthesis in mammals and improve the reproductive performance. However, the effect of NCG on poultry laying performance is still unclear. This study investigated the effect of dietary NCG on development of chicken ovarian follicles. The dosage and timing for NCG administration were evaluated for its effect on follicular development. Results showed that supplementation with 1% NCG in the diet for 14 D led to accelerated development of growing follicles (over 60 μm in oocyte diameter) and significantly increased feed intake and feed efficiency. Plasma amino acids (AA) analysis showed that feeding with 1% NCG significantly increased of plasma AA levels. RNA-seq analysis revealed that NCG supplementation upregulated expression of genes related to angiogenesis and cell proliferation, but downregulated expression of apoptosis-related genes. Meanwhile, RT-qPCR and Western blot analysis validated the RNA-seq results. Moreover, NCG enhanced plasma NO level; upregulated expression of PKG-I, Raf1, and p-p38; and increased angiogenesis of the ovaries. In conclusion, dietary NCG (1% for 14 D) can promote development of ovarian follicles by increasing angiogenesis in ovaries of the chicken.

A robustness metric for biological data clustering algorithms

BACKGROUND

Cluster analysis is a core task in modern data-centric computation. Algorithmic choice is driven by factors such as data size and heterogeneity, the similarity measures employed, and the type of clusters sought. Familiarity and mere preference often play a significant role as well. Comparisons between clustering algorithms tend to focus on cluster quality. Such comparisons are complicated by the fact that algorithms often have multiple settings that can affect the clusters produced. Such a setting may represent, for example, a preset variable, a parameter of interest, or various sorts of initial assignments. A question of interest then is this: to what degree do the clusters produced vary as setting values change?

RESULTS

This work introduces a new metric, termed simply "robustness", designed to answer that question. Robustness is an easily-interpretable measure of the propensity of a clustering algorithm to maintain output coherence over a range of settings. The robustness of eleven popular clustering algorithms is evaluated over some two dozen publicly available mRNA expression microarray datasets. Given their straightforwardness and predictability, hierarchical methods generally exhibited the highest robustness on most datasets. Of the more complex strategies, the paraclique algorithm yielded consistently higher robustness than other algorithms tested, approaching and even surpassing hierarchical methods on several datasets. Other techniques exhibited mixed robustness, with no clear distinction between them.

CONCLUSIONS

Robustness provides a simple and intuitive measure of the stability and predictability of a clustering algorithm. It can be a useful tool to aid both in algorithm selection and in deciding how much effort to devote to parameter tuning.

Acylated Ghrelin Supports the Ovarian Transcriptome and Follicles in the Mouse: Implications for Fertility

Ghrelin, an orexigenic gut-derived peptide, is gaining increasing attention due to its multifaceted role in a number of physiological functions, including reproduction. Ghrelin exists in circulation primarily as des-acylated and acylated ghrelin. Des-acyl ghrelin, until recently considered to be an inactive form of ghrelin, is now known to have independent physiological functionality. However, the relative contribution of acyl and des-acyl ghrelin to reproductive development and function is currently unknown. Here we used ghrelin-O-acyltransferase (GOAT) knockout (KO) mice that have no measurable levels of endogenous acyl ghrelin and chronically high levels of des-acyl ghrelin, to characterize how the developmental and life-long absence of acyl ghrelin affects ovarian development and reproductive capacity. We combined the assessment of markers of reproductive maturity and the capacity to breed with measures of ovarian morphometry, as well as with ovarian RNA sequencing analysis. Our data show that while GOAT KO mice retain the capacity to breed in young adulthood, there is a diminished number of ovarian follicles (per mm³) in the juvenile and adult ovaries, due to a significant reduction in the number of small follicles, particularly the primordial follicles. We also show pronounced specific changes in the ovarian transcriptome in the juvenile GOAT KO ovary, indicative of a potential for premature ovarian development. Collectively, these findings indicate that an absence of acyl ghrelin does not prevent reproductive success but that appropriate levels of acyl and des-acyl ghrelin may be necessary for optimal ovarian maturation.

Trichloroethylene-induced alterations in DNA methylation were enriched in polycomb protein binding sites in effector/memory CD4+ T cells

Exposure to industrial solvent and water pollutant trichloroethylene (TCE) can promote autoimmunity, and expand effector/memory (CD62L) CD4+ T cells. In order to better understand etiology reduced representation bisulfite sequencing was used to study how a 40-week exposure to TCE in drinking water altered methylation of ∼337 770 CpG sites across the entire genome of effector/memory CD4+ T cells from MRL+/+ mice. Regardless of TCE exposure, 62% of CpG sites in autosomal chromosomes were hypomethylated (0-15% methylation), and 25% were hypermethylated (85-100% methylation). In contrast, only 6% of the CpGs on the X chromosome were hypomethylated, and 51% had mid-range methylation levels. In terms of TCE impact, TCE altered (≥ 10%) the methylation of 233 CpG sites in effector/memory CD4+ T cells. Approximately 31.7% of these differentially methylated sites occurred in regions known to bind one or more Polycomb group (PcG) proteins, namely Ezh2, Suz12, Mtf2 or Jarid2. In comparison, only 23.3% of CpG sites not differentially methylated by TCE were found in PcG protein binding regions. Transcriptomics revealed that TCE altered the expression of ∼560 genes in the same effector/memory CD4+ T cells. At least 80% of the immune genes altered by TCE had binding sites for PcG proteins flanking their transcription start site, or were regulated by other transcription factors that were in turn ordered by PcG proteins at their own transcription start site. Thus, PcG proteins, and the differential methylation of their binding sites, may represent a new mechanism by which TCE could alter the function of effector/memory CD4+ T cells.

Muscle-specific downregulation of GR levels inhibits adipogenesis in porcine intramuscular adipocyte tissue

Intramuscular adipose is conducive to good pork quality, whereas subcutaneous adipose is considered as waste in pig production. So uncovering the regulation differences between these two adiposes is helpful to tissue-specific control of fat deposition. In this study, we found the sensitivity to glucocorticoids (GCs) was lower in intramuscular adipocytes (IMA) compared with subcutaneous adipocytes (SA). Comparison of glucocorticoid receptor (GR) revealed that IMA had lower GR level which contributed to its reduced GCs sensitivity. Higher methylation levels of GR promotor 1-C and 1-H were detected in IMA compared with SA. GR expression decrease was also found in adipocytes when treated with muscle conditioned medium (MCM) in vitro, which resulted in significant inhibition of adipocytes proliferation and differentiation. Since abundant myostatin (MSTN) was detected in MCM by ELISA assay, we further investigated the effect of this myokine on adipocytes. MSTN treatment suppressed adipocytes GR expression, cell proliferation and differentiation, which mimicked the effects of MCM. The methylation levels of GR promotor 1-C and 1-H were also elevated after MSTN treatment. Our study reveals the role of GR in muscle fiber inhibition on intramuscular adipocytes, and identifies myostatin as a muscle-derived modulator for adipose GR level.

Energetic Effects of Pre-hatch Albumen Removal on Embryonic Development and Early Ontogeny in Gallus gallus

Studies on the yolk and albumen content in bird eggs, and the effects of variations in their relative loads in the phenotype of the birds, have revealed multiple consequences at different levels of biological organization, from biochemical traits to behavior. However, little is known about the effect of albumen variation on energetics performance during development and early ontogeny, despite the fact that variation in energy expenditure may have consequences in terms of fitness for both feral and domestic species. In this work, we evaluated experimentally whether variations in the content of albumen of Gallus gallus eggs could generate differences in metabolic rates during embryonic development. Additionally, we assessed changes in the activity of mitochondrial enzymes (cytochrome c oxidase and citrate synthase) in skeletal muscles and liver. Finally, we evaluated the success of hatching of these embryos and their metabolic rates (MR) post-hatching. The results revealed a significant reduction in MR in the last fifth of embryonic life, and reduced catabolic activities in the skeletal muscle of chicks hatched from albumen-removed eggs. However, the same group demonstrated an increase in catabolic activity in the liver, suggesting the existence of changes in energy allocation between tissues. Besides, we found a decrease in hatching success in the albumen-removed group, suggesting a negative effect of the lower albumen content on eggs, possibly due to lower catabolic activities in skeletal muscle. We also found a compensatory phenomenon in the first week after hatching, i.e., birds from albumen-removed eggs did not show a decrease in MR either at thermoneutral temperatures or at 10°C, compared to the control group. Collectively, our data suggest that a reduction in albumen may generate a trade-off between tissue metabolic activities, and may explain the differences in metabolic rates and hatching success, supporting the immediate adaptive response (IAR) hypothesis.