[Comparative analysis on content and distribution of CpG sites in milk production traits and mastitis-related genes in dairy cattle]

How Does Nutrition Affect the Epigenetic Changes in Dairy Cows?

Dairy cows require a balanced diet that provides enough nutrients to support milk production, growth, and reproduction. Inadequate nutrition can lead to metabolic disorders, impaired fertility, and reduced milk yield. Recent studies have shown that nutrition can affect epigenetic modifications in dairy cows, which can impact gene expression and affect the cows' health and productivity. One of the most important epigenetic modifications in dairy cows is DNA methylation, which involves the addition of a methyl group to the DNA molecule. Studies have shown that the methylation status of certain genes in dairy cows can be influenced by dietary factors such as the level of methionine, lysine, choline, and folate in the diet. Other important epigenetic modifications in dairy cows are histone modification and microRNAs as regulators of gene expression. Overall, these findings suggest that nutrition can have a significant impact on the epigenetic regulation of gene expression in dairy cows. By optimizing the diet of dairy cows, it may be possible to improve their health and productivity by promoting beneficial epigenetic modifications. This paper reviews the main nutrients that can cause epigenetic changes in dairy cattle by analyzing the effect of diet on milk production and its composition.

Analysis of Methylation and mRNA Expression of Lin28B Gene Promoter Region in the Hypothalamus of Dolang Sheep During Pubertal Initiation

Lin28B plays an important role in puberty initiation in sheep. This study aimed to discuss the correlation between different growth periods and the methylation status of cytosine-guanine dinucleotide (CpG) islands in the promoter region of the Lin28B gene in the Dolang sheep's hypothalamus. In this study, the sequence of the Lin28B gene promoter region in Dolang sheep was obtained by cloning and sequencing, and methyl groups of the CpG island of the Lin28B gene promoter in the hypothalamus were detected by bisulfite sequencing PCR during the three periods of prepuberty, adolescence, and postpuberty in Dolang sheep. Lin28B expression in the Dolang sheep's hypothalamus was detected by fluorescence quantitative PCR at three stages: prepuberty, puberty, and postpuberty. In this experiment, the 2993-bp Lin28B promoter region was obtained, and it was predicted that there was a CpG island containing 15 transcription factor binding sites and 12 CpG sites, which may play a role in gene expression regulation. Overall, methylation levels increased from prepuberty to postpuberty, while Lin28B expression levels decreased, indicating that Lin28B expression was negatively correlated with promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG5, CpG7, and CpG9 between pre- and postpuberty (p < 0.05). Our data show that Lin28B expression is increased by demethylation of promoter CpG islands, with CpG5, CpG7, and CpG9 implicated as critical regulatory sites.

Prediction of the Effect of Methylation in the Promoter Region of ZP2 Gene on Egg Production in Jinghai Yellow Chickens

Egg production in chickens is a quantitative trait. The aim of this study was to investigate the effect of promoter methylation of the Zona pellucida 2 (ZP2) gene on egg production. Real-time fluorescence quantification showed that the expression of the ZP2 gene in the ovaries of 300-day-old Jinghai yellow chickens in the high-laying group was significantly higher than that in the low-laying group (p < 0.01). A series of deletion fragments of the ZP2 gene promoter in Jinghai yellow chickens had different promoter activities in DF-1 cells, and the core region of the ZP2 gene promoter was found to be between −1552 and −1348. Four CpG islands in the promoter region of the ZP2 gene were detected by software prediction. The overall degree of methylation of the ZP2-1 amplified fragment was negatively correlated with mRNA expression to some extent (R = −0.197); the overall degree of methylation of the ZP2-2 amplified fragment was also negatively correlated with mRNA expression to some extent (R = −0.264), in which the methylation of methylcytosine (mC)-9, mC-20, and mC-21 sites was significantly negatively correlated with mRNA expression (p < 0.05). In addition, the mC-20 and mC-21 sites are located on the Sp1 transcription factor binding site, and it is speculated that these two sites may be the main sites for regulating transcription. In summary, the methylation sites mC-20 and mC-21 of the ZP2 gene may inhibit the binding of Sp1 and DNA, affect the transcription of the ZP2 gene, and then affect the number of eggs produced by the Jinghai yellow chickens.

MRVI1 and NTRK3 Are Potential Tumor Suppressor Genes Commonly Inactivated by DNA Methylation in Cervical Cancer

The abnormally methylated tumor suppressor genes (TSGs) associated with cervical cancer are unclear. DNA methylation data, RNA-seq expression profiles, and overall survival data were downloaded from TCGA CESC database. DMGs and DEGs were obtained through CHAMP and DESeq packages, respectively. TSGs were downloaded from TSGene 2.0. Candidate hypermethylated/down-regulated TSGs were further evaluated and pyrosequencing was used to confirm their difference in methylation levels of selected TSGs in cervical cancer patients. A total of 25946 differentially methylated CpGs corresponding to 2686 hypermethylated genes and 4898 hypomethylated genes between cervical cancer and adjacent normal cervical tissues were found in this study. Besides, 693 DEGs (109 up-regulated and 584 down-regulated) were discovered in cervical cancer tissues. Then, 192 hypermethylated/down-regulated genes were obtained in cervical cancer compared to adjacent tissues. Interestingly, 26 TSGs were found in hypermethylated/down-regulated genes. Among these genes, low expression of MRVI1 and NTRK3 was associated with poor overall survival in cervical cancer. Moreover, GEO data showed that MRVI1 and NTRK3 were significantly decreased in cervical cancer tissues. The expression levels of MRVI1 and NTRK3 were negatively correlated with the methylation levels of their promoter CpG sites. Additionally, elevated methylation levels of MRVI1 and NTRK3 promoter were further verified in cervical cancer tissues by pyrosequencing experiments. Finally, the ROC results showed that the promoter methylation levels of MRVI1 and NTRK3 had the ability to discriminate cervical cancer from healthy samples. The study contributes to our understanding of the roles of MRVI1 and NTRK3 in cervical cancer.

DNA Methylation of Pig FUT3 Promoter Alters mRNA Expression to Regulate E. coli F18 Susceptibility

Post-weaning diarrhea (PWD) is frequently associated with E. coli F18 infections in piglets. However, the underlying molecular mechanism concerning the resistance of E. coli F18 in local weaned piglets in China is not clearly understood. In the present study, by a comparative analysis of the transcriptome, a-1,3-fucosyltransferase (FUT3) was evaluated as a key candidate correlated with resistance to E. coli F18 in Sutai and Meishan piglets. Functional analysis demonstrated that FUT3 acts as a key positive regulator of E. coli F18 susceptibility in newly food accustomed piglets. However, the core promoter of FUT3 was present at −500–(−206) bp (chr.2: g.73171117–g.73171616), comprising of 9 methylated CpG sites. Among these, the methylation levels of the two CpG sites (mC-3, mC-5) located in HIF1A and Sp1 transcription factor (TF) considerably associated with mRNA expression of FUT3 (p < 0.05). Our findings indicated that the methylation of mC-3 and mC-5 sites has certain inhibitory effect on FUT3 expression and promotes the resistance of E. coli F18 in piglets. The underlined study may explore FUT3 as a new candidate target in E. coli F18 infection in Chinese local weaned piglets.

Regulatory Effect of Methylation of the Porcine AQP3 Gene Promoter Region on Its Expression Level and Porcine Epidemic Diarrhea Virus Resistance

As an important carrier for intestinal secretion and water absorption, aquaporin 3 (AQP3) is closely related to diarrhea. In this study, we investigated the mechanisms of AQP3 gene expression regulation in porcine epidemic diarrhea virus (PEDV)-induced diarrhea confirmed by PCR amplification and sequencing. Evaluation of intestinal pathology showed that diarrhea caused by PEDV infection destroyed the intestinal barrier of piglets. qPCR analysis showed that AQP3 expression in the small intestine of PEDV-infected piglets was extremely significantly decreased. qPCR and Bisulfite sequencing PCR revealed an increase in the methylation levels of both CpG islands in the AQP3 promoter region in the jejunum of PEDV-infected piglets. The methylation of mC-20 and mC-10 sites within the two CpG islands showed a significant negative correlation with AQP3 expression. Chromatin Co-Immunoprecipitation (ChIP)-PCR showed that the Sp1 transcription factor was bound to the AQP3 promoter region containing these two CpG sites. AQP3 expression was also extremely significantly reduced in Sp1-inhibited IPEC-J2 cells, indicating that abnormal methylation at the mC-20 site of CpG1 and the mC-10 site of CpG2 reduces its expression in PEDV-infected piglet jejunum by inhibiting the binding of Sp1 to the AQP3 promoter. These findings provide a theoretical basis for further functional studies of porcine AQP3.

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.

Age-associated methylation change of CHI promoter in herbaceous peony (Paeonia lactiflora Pall)

Chalcone isomerase gene (CHI) is a key gene that regulates the formation of yellow traits in petals. To reveal transcriptional regulatory mechanisms of CHI gene in petals of Paeonia lactiflora, we investigated the CHI expression using qPCR, the pigment content by HPLC, and methylation levels using BSP+Miseq sequencing in ‘Huangjinlun’ variety during different developmental stages including flower-bud stage (S1), initiating bloom (S2), bloom stage (S3), and withering stage (S4). Results showed that the expression level of CHI gene at S2 stage was significantly higher than that at other stages (P<0.05), and at S4 stage was extremely significantly lower than other stages (P<0.01). Besides, total anthocyanin, anthoxanthin, and flavonoid contents in petals presented a similar trend with CHI expression during developmental stages. A total of 16 CpG sites varying methylation levels were detected in CHI gene core promoter region, of which the methylation levels at mC-4 and mC-16 sites were extremely significantly negatively correlated with CHI mRNA expression (P<0.01). mC-16 site is located in the binding region of C/EBPα transcription factor, suggesting that methylation at the mC-16 site may inhibit the binding of C/EBPα to CHI promoter DNA, thereby regulating the tissue-specific expression of CHI gene. Our study revealed the expression pattern of CHI gene in petal tissues of P. lactiflora at different developmental stages, which is related to promoter methylation. Moreover, the important transcription regulation element–C/EBPα was identified, providing theoretical reference for in-depth study on the function of CHI gene in P. lactiflora.

New Insight into the Molecular Mechanism of the FUT2 Regulating Escherichia coli F18 Resistance in Weaned Piglets

Escherichia coli (E. coli) F18 is the main pathogen responsible for post-weaning diarrhea (PWD) in piglets. Resistance to E. coli F18 depends on the expression of the cognate receptors in the intestinal epithelial cells. However, the molecular mechanism of E. coli F18 resistance in weaned piglets remains unclear. Here, we performed a comparative transcriptome study of the duodenal tissue from Sutai E. coli F18 sensitive and resistant pigs by RNA-seq, and pig α(1,2) fucosyltransferase 2 (FUT2) was identified as a host differentially expressed gene controlling the E. coli F18 infection. Function analysis showed that the FUT2 expression was high in the duodenum and jejunum, with higher levels detected in sensitive individuals than in resistant individuals (p < 0.01). Expression levels of FUT2 were upregulated in IPEC-J2 cells after lipopolysaccharide (LPS)-induction or E. coli stimulation. FUT2 knockdown decreased the adhesion of E. coli F18 to IPEC-J2 cells (p < 0.05). FUT2 overexpression markedly increased the adhesion of E. coli F18 to IPEC-J2 cells (p < 0.05 or p < 0.01). Furthermore, the FUT2 mRNA levels correlated with methylation levels of the mC-22 site in the specificity protein 1 (Sp1) transcription factor (p < 0.05). Electrophoretic mobility shift assays (EMSA) showed that Sp1 interacts with the wild-type FUT2 promoter DNA, but not with methylated DNA. Our data suggested that FUT2 methylation at the mC-22 site inhibits Sp1 binding to the FUT2 promoter, thereby reducing FUT2 expression and enhancing E. coli F18 resistance in weaned piglets. These observations highlight FUT2 as a promising new target for combating E. coli F18 susceptibility in weaned piglets.

Transcriptional Suppression of Renal Antioxidant Enzyme Systems in Guinea Pigs Exposed to Polymerized Cell-Free Hemoglobin

Hemoglobin-based oxygen carriers (HBOCs) are being developed as oxygen and plasma volume-expanding therapeutics though their potential to promote oxidative tissue injury has raised safety concerns. Using a guinea pig exchange transfusion model, we examined the effects of polymerized bovine hemoglobin (HbG) on the transcriptional regulation, activity, and expression of the renal antioxidant enzymes; superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). HbG infusion downregulated the mRNA levels for genes encoding SOD isoforms 1-3, GPx1, GPx3, GPx4, and CAT. This transcriptional suppression correlated with decreased enzymatic activities for SOD, CAT, and GPx. Immunostaining revealed decreased protein expression of SOD1, CAT, and GPx1 primarily in renal cortical tubules. DNA methylation analyses identified CpG hypermethylation in the gene promoters for SOD1-3, GPx1, GPx3, and GPx4, suggesting an epigenetic-based mechanism underlying the observed gene repression. HbG also induced oxidative stress as evidenced by increased renal lipid peroxidation end-products and 4-HNE immunostaining, which could be the result of the depleted antioxidant defenses and/or serve as a trigger for increased DNA methylation. Together, these findings provide evidence that the renal exposure to HbG suppresses the function of major antioxidant defense systems which may have relevant implications for understanding the safety of hemoglobin-based products.

Age-associated methylation change of TAP1 promoter in piglet

Diarrhea and edematous disease are two major causes of mortality in postweaning piglets. These conditions lead to huge economic losses in the swine industry. Escherichia coli F18 is the primary causative agent of these two diseases. Transported associated with antigen processing (TAP) plays an important role in the immune response and the TAP1 gene could be an effective anti-E. coli F18 molecular marker in pigs. The aim of this study was to determine the correlation between TAP1 gene promoter CpG island methylation status and mRNA expression in piglets. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the TAP1 gene promoter CpG islands and fluorescence quantitative PCR was used to detect TAP1 expression in the jejunum of Sutai piglets from birth to weaning age. The fragment of the TAP1 gene promoter region under investigation has no mutation, has 13 putative transcription factor binding sites containing 19 CpG sites, and may be important for regulation of gene expression. With increasing age, the overall methylation levels decreased, while the TAP1 expression levels increased, indicating a negative correlation between TAP1 expression and promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG_4, CpG_13 and CpG_15 among the different age groups (P<0.05). Our data indicate that TAP1 expression is increased by demethylation of promoter CpG islands, with CpG_4, CpG_13 and CpG_15 implicated as the critical regulatory sites.

Correlation between BPI gene upstream CpG island methylation and mRNA expression in piglets

Diarrhea and edematous disease are two major causes of mortality in postweaning piglets, and these conditions lead to huge economic losses in the swine industry. E. coli F18 is the primary causative agent of these two diseases. Bactericidal/permeability-increasing protein (BPI) plays an important role in the natural defense of the host. The aim of this study was to determine the correlation between BPI gene upstream CpG island methylation and mRNA expression. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the BPI gene upstream CpG island and fluorescence quantitative PCR was used to detect BPI expression in the duodenum of piglets from birth to weaning age. BPI upstream CpG islands were shown to have many putative transcription factor binding sites, 10 CpG sites and every CpG site was methylated. The CpG island methylation level was lowest in 30-day piglets and was significantly lower than levels in 8-day piglets (p < 0.05). BPI mRNA expression was significantly higher in 30-day piglets than at any other age (p < 0.05). Pearson’s correlation analysis showed that the methylation status of the CpG island was negatively correlated with BPI mRNA expression. Statistical significances were found in CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 (p < 0.05). The data indicate that BPI expression is improved by demethylation of the BPI gene upstream CpG island. Furthermore, CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 may be critical sites in the regulation of BPI gene expression.