Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication

Differential DNA Methylation and Gene Expression Between ALV-J-Positive and ALV-J-Negative Chickens

Background: Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic losses in the poultry industry; unfortunately, there is no effective vaccine against ALV-J. DNA methylation plays a crucial role in several biological processes, and an increasing number of diseases have been proven to be related to alterations in DNA methylation. In this study, we screened ALV-J-positive and -negative chickens. Subsequently, we generated and provided the genome-wide gene expression and DNA methylation profiles by MeDIP-seq and RNA-seq of ALV-J-positive and -negative chicken samples; 8,304 differentially methylated regions (DMRs) were identified by MeDIP-seq analysis (p ≤ 0.005) and 515 differentially expressed genes were identified by RNA-seq analysis (p ≤ 0.05). As a result of an integration analysis, we screened six candidate genes to identify ALV-J-negative chickens that possessed differential methylation in the promoter region. Furthermore, TGFB2 played an important role in tumorigenesis and cancer progression, which suggested TGFB2 may be an indicator for identifying ALV-J infections.

DNA methylation status of SERPINA3 gene involved in mRNA expression in three cattle breeds

DNA methylation could take part in the gene expression and acts an important role in muscle development. In this study, DNA methylation and expression in adipose and muscle tissues were examined at the same time to evaluate the extent of epigenetic modifications and gene expression on the differentially methylated region (DMR) in SERPINA3. Chain reaction of bisulfite sequencing polymerase (BSP) was used to compared difference among DNA methylation patterns. The result of quantitative real-time PCR (qPCR) analysis showed that there was an extensive expression of SERPINA3 gene in tissue and there was a significant difference existing in muscle and adipose between Jiaxian cattle and individual of other breeds with increasing hybridization (p < 0.05). The statistic analyses indicated that DNA methylation patterns had a significant influence to the level of mRNA in tissue of fat and muscle. This study may be an important reference for investigating development of muscle tissue in cattle, and may promote the process of cattle molecular breeding.

A chicken DNA methylation clock for the prediction of broiler health

The domestic chicken (Gallus gallus domesticus) is the globally most important source of commercially produced meat. While genetic approaches have played an important role in the development of chicken stocks, little is known about chicken epigenetics. We have systematically analyzed the chicken DNA methylation machinery and DNA methylation landscape. While overall DNA methylation distribution was similar to mammals, sperm DNA appeared hypomethylated, which correlates with the absence of the DNMT3L cofactor in the chicken genome. Additional analysis revealed the presence of low-methylated regions, which are conserved gene regulatory elements that show tissue-specific methylation patterns. We also used whole-genome bisulfite sequencing to generate 56 single-base resolution methylomes from various tissues and developmental time points to establish an LMR-based DNA methylation clock for broiler chicken age prediction. This clock was used to demonstrate epigenetic age acceleration in animals with experimentally induced inflammation. Our study provides detailed insights into the chicken methylome and suggests a novel application of the DNA methylation clock as a marker for livestock health.

Raddatz, Lyko and colleagues use whole-genome bisulfite sequencing data to generate a methylation clock for chicken. This clock was able to detect age acceleration in broiler chickens under experimentally induced inflammation.

Whole-genome bisulfite sequencing of abdominal adipose reveals DNA methylation pattern variations in broiler lines divergently selected for fatness

The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3' untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken

Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported. Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments. Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments. Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.

Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the SLCO1B3, RNA Expression and Color Change in Blue Eggshells in Lushi Chickens

The formation mechanism underlying the blue eggshell characteristic has been discovered in birds, and SLCO1B3 is the key gene that regulates the blue eggshell color. Insertion of an endogenous retrovirus, EAV-HP, in the SLCO1B3 5′ flanking region promotes SLCO1B3 expression in the chicken shell gland, and this expression causes bile salts to enter the shell gland, where biliverdin is secreted into the eggshell, forming a blue shell. However, at different laying stages of the same group of chickens, the color of the eggshell can vary widely, and the molecular mechanism underlying the eggshell color change remains unknown. Therefore, to reveal the molecular mechanism of the blue eggshell color variations, we analyzed the change in the eggshell color during the laying period. The results indicated that the eggshell color in Lushi chickens can be divided into three stages: 20–25 weeks for dark blue, 26–45 weeks for medium blue, and 46–60 weeks for light blue. We further investigated the expression and methylation levels of the SLCO1B3 gene at eight different weeks, finding that the relative expression of SLCO1B3 was significantly higher at 25 and 30 weeks than at other laying weeks. Furthermore, the overall methylation rate of the SLCO1B3 gene in Lushi chickens increased gradually with increasing weeks of egg production, as shown by bisulfite sequencing PCR. Pearson correlation analysis showed that methylation of the promoter region of SLCO1B3 was significantly negatively correlated with both SLCO1B3 expression in the shell gland tissue and eggshell color. In addition, we predicted that CpG5 and CpG8 may be key sites for regulating SLCO1B3 gene transcription. Our findings show that as the level of methylation increases, methylation of the CpG5 and CpG8 sites hinders the binding of transcription factors to the promoter, reducing SLCO1B3 expression during the late period and resulting in a lighter eggshell color.

Changes of host DNA methylation in domestic chickens infected with Salmonella enterica

Cytosine methylation is an effective way to modulate gene transcription.However, very little is knownabout the epigenetic changes in the host that is infected with Salmonella enterica. In this study, we usedmethylatedDNA immunoprecipitation sequencing to analyse the genomewide DNA methylation changes in domestic chickens after infected with Salmonella. The level of DNA methylation was slightly higher in the genomic regions around the transcription start termination sites in a Salmonella-infected group compared to the controls. Overall, 879 peaks were differentially methylated between Salmonella-infected and control groups, among which 135 were located in the gene promoter regions. Genes including MHC class IV antigen, GABARAPL1, MR1 and KDM1B were shown to be methylated more heavily after infected with Salmonella, whereas DYNLRB2, SEC14L3 and ANKIB1 tended to have fewer methylated cytosine residues in the promoter regions.Gene interaction network analysis of differentiallymethylated genes in the promoter regions revealed extensive connections with immune-related genes, indicating the possible impact of infection with Salmonella on the epigenetic status of the host.

Transcription-Associated Mutation Promotes RNA Complexity in Highly Expressed Genes-A Major New Source of Selectable Variation

Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens, and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces 10-fold more isoforms than expected from the number of splice junctions in the genome. These isoforms were produced mainly by alternative use of de novo splice sites generated by transcription-associated mutation (TAM), not by the RNA editing mechanism normally invoked. We found that high expression of globin genes increases mutation frequencies during transcription, especially on nontranscribed DNA strands. After DNA replication, transcribed strands inherit these somatic mutations, creating de novo splice sites, and generating multiple distinct isoforms in the cell clone. Bisulfate sequencing revealed that DNA methylation may counteract this process by suppressing TAM, suggesting DNA methylation can spatially regulate RNA complexity. RNA profiling showed that falcons living on the high Qinghai-Tibetan Plateau possess greater global gene expression levels and higher diversity of mean to high abundance isoforms (reads per kilobases per million mapped reads ≥18) than their low-altitude counterparts, and we speculate that this may enhance their oxygen transport capacity under low-oxygen environments. Thus, TAM-induced RNA diversity may be physiologically significant, providing an alternative strategy in lifestyle evolution.

DNA methylation profiles correlated to striped bass sperm fertility

Background

Striped bass (Morone saxatilis) spermatozoa are used to fertilize in vitro the eggs of white bass (M. chrysops) to produce the preferred hybrid for the striped bass aquaculture industry. Currently, only one source of domestic striped bass juveniles is available to growers that is not obtained from wild-caught parents and is thus devoid of any genetic improvement in phenotypic traits of importance to aquaculture. Sperm epigenetic modification has been predicted to be associated with fertility, which could switch genes on and off without changing the DNA sequence itself. DNA methylation is one of the most common epigenetic modification types and changes in sperm epigenetics can be correlated to sub-fertility or infertility in male striped bass. The objective of this study was to find the differentially methylated regions (DMRs) between high-fertility and sub-fertility male striped bass, which could potentially regulate the fertility performance.

Results

In our present study, we performed DNA methylation analysis of high-fertility and sub-fertility striped bass spermatozoa through MBD-Seq methods. A total of 171 DMRs were discovered in striped bass sperm correlated to fertility. Based on the annotation of these DMRs, we conducted a functional classification analysis and two important groups of genes including the WDR3/UTP12 and GPCR families, were discovered to be related to fertility performance of striped bass. Proteins from the WDR3/UTP12 family are involved in forming the sperm flagella apparatus in vertebrates and GPCRs are involved in hormonal signaling and regulation of tissue development, proliferation and differentiation.

Conclusions

Our results contribute insights into understanding the mechanism of fertility in striped bass, which will provide powerful tools to maximize reproductive efficiencies and to identify those males with superior gametes for this important aquaculture species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4548-6) contains supplementary material, which is available to authorized users.

Evaluation of DNA methylation and mRNA expression of heat shock proteins in thermal manipulated chicken

Thermal manipulation during embryogenesis has been demonstrated to enhance the thermotolerance capacity of broilers through epigenetic modifications. Heat shock proteins (HSPs) are induced in response to stress for guarding cells against damage. The present study investigates the effect of thermal conditioning during embryogenesis and thermal challenge at 42 days of age on HSP gene and protein expression, DNA methylation and in vitro luciferase assay in brain tissue of Naked Neck (NN) and Punjab Broiler-2 (PB-2) chicken. On the 15th day of incubation, fertile eggs from two breeds, NN and PB-2, were randomly divided in to two groups: control (C)-eggs were incubated under standard incubation conditions, and thermal conditioning (TC)-eggs were exposed to higher incubation temperature (40.5°C) for 3 h on the 15th, 16th, and 17th days of incubation. The chicks obtained from each group were further subdivided and reared under different environmental conditions from the 15th to the 42nd day as normal [N; 25 ± 1 °C, 70% relative humidity (RH)] and heat exposed (HE; 35 ± 1 °C, 50% RH) resulting in four treatment groups (CN, CHE, TCN, and TCHE). The results revealed that HSP promoter activity was stronger in CHE, which had lesser methylation and higher gene expression. The activity of promoter region was lesser in TCHE birds that were thermally manipulated at the embryonic stage, thus reflecting their stress-free condition. This was confirmed by the lower level of mRNA expression of all the HSP genes. In conclusion, thermal conditioning during embryogenesis has a positive impact and improves chicken thermotolerance capacity in postnatal life.

Caloric restriction delays age-related methylation drift

In mammals, caloric restriction consistently results in extended lifespan. Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites. Here, we report that epigenetic drift is conserved across species and the rate of drift correlates with lifespan when comparing mice, rhesus monkeys, and humans. Twenty-two to 30-year-old rhesus monkeys exposed to 30% caloric restriction since 7–14 years of age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation age appeared 7 years younger than their chronologic age. Even more pronounced effects were seen in 2.7–3.2-year-old mice exposed to 40% caloric restriction starting at 0.3 years of age. The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene expression. We propose that epigenetic drift is a determinant of lifespan in mammals.

Caloric restriction has been shown to increase lifespan in mammals. Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in mice and rhesus monkeys results in attenuation of age-related methylation drift.

Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens

Poultry meat quality is associated with breed, age, tissue and other factors. Many previous studies have focused on distinct breeds; however, little is known regarding the epigenetic regulatory mechanisms in different age stages, such as DNA methylation. Here, we compared the global DNA methylation profiles between juvenile (20 weeks old) and later laying-period (55 weeks old) hens and identified candidate genes related to the development and meat quality of breast muscle using whole-genome bisulfite sequencing. The results showed that the later laying-period hens, which had a higher intramuscular fat (IMF) deposition capacity and water holding capacity (WHC) and less tenderness, exhibited higher global DNA methylation levels than the juvenile hens. A total of 2,714 differentially methylated regions were identified in the present study, which corresponded to 378 differentially methylated genes, mainly affecting muscle development, lipid metabolism, and the ageing process. Hypermethylation of the promoters of the genes ABCA1, COL6A1 and GSTT1L and the resulting transcriptional down-regulation in the later laying-period hens may be the reason for the significant difference in the meat quality between the juvenile and later laying-period hens. These findings contribute to a better understanding of epigenetic regulation in the skeletal muscle development and meat quality of chicken.