Regulation of DNA methylation during the testicular development of Shaziling pigs

Yang, Anqi; Yan, Saina; Chujie, Chen; Yin, Yulong; Tang, Xiangwei; Jiajia, Ma; Xiang, Jiaojiao; Ran, Maoliang; Chen, Bin

doi:10.1016/j.ygeno.2022.110450

Cited by 7 publications

(13 citation statements)

References 127 publications

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“…According to our combined analysis results, overall, the non-CpG methylation levels in promoters and gene bodies were negatively and positively correlated with gene expression, respectively. This was similar to DNA methylation in CpG contexts [ 15 ], which indicates that DNA methylation in both CpG contexts and non-CpG contexts might own the same regulatory mechanism in gene expression. DNA methylation and demethylation can change the accessibility of the promoter and can affect the recruitment of DNA-binding proteins.…”

Section: Discussionmentioning

confidence: 58%

“…In previous studies, we have reviewed testicular genomic methylation patterns at different developmental stages, and it is generally believed that the sequencing data for the samples have good repeatability at the global level of the methylation levels [ 15 ]. Therefore, in the present study, we directly performed a series of analyses on the potential regulatory mechanisms of non-CpG methylation during testicular maturation.…”

Section: Resultsmentioning

confidence: 99%

“…For example, 5mC at CpA sites accounts for approximately 25% of all 5mC in human embryonic stem cells, whereas the proportion of those in human fibroblast cell lines is negligible [ 21 ]. In the porcine testicular genome, non-CpG methylation levels averaged 1.06% [ 15 ]. However, recent studies have reported that a high proportion of non-CpG methylation is also present in differentiated cells, for example, brain tissue [ 22 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

“…Both WGBS and RNA-seq libraries were constructed on an Illumina Novaseq 6000, by Novogene Corporation (Beijing, China), and 150 bp paired-end reads were generated. An overview of the basic analysis of WGBS and RNA-seq were conducted in our past research, and differentially expressed genes (DEGs) in two developmental stages were also identified [ 15 ]. The raw sequence data of WGBS and RNA-seq obtained in our previous studies was deposited in the Genome Sequence Archive (Genomics, Proteomics and Bioinformatics, 2021), in National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation/Beijing Institute of Genomics, and Chinese Academy of Sciences (GSA: CRA009180 and CRA009195).…”

Section: Methodsmentioning

confidence: 99%

“…Our recent research showed that DNA methylation in CpG contexts that are associated with promoters and gene bodies affects the proliferation and differentiation of testicular cells by regulating the gene expression [ 15 ]. However, the regulatory mechanisms of non-CpG methylation during testicular development were not elucidated in our past research; therefore, in this study, we re-analyzed the data from the whole-genome bisulfite sequencing (WGBS) in order to identify the differentially methylated regions (DMRs) and the differentially methylated genes (DMGs) in non-CpG contexts, between the 1- and 75-day-old stages.…”

Section: Introductionmentioning

confidence: 99%

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FZD7, Regulated by Non-CpG Methylation, Plays an Important Role in Immature Porcine Sertoli Cell Proliferation

Yang

Yan

Yin

et al. 2023

IJMS

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The regulatory role of non-CpG methylation in mammals has been important in whole-genome bisulfite sequencing. It has also been suggested that non-CpG methylation regulates gene expression to affect the development and health of mammals. However, the dynamic regulatory mechanisms of genome-wide, non-CpG methylation during testicular development still require intensive study. In this study, we analyzed the dataset from the whole-genome bisulfite sequencing (WGBS) and the RNA-seq of precocious porcine testicular tissues across two developmental stages (1 and 75 days old) in order to explore the regulatory roles of non-CpG methylation. Our results showed that genes regulated by non-CpG methylation affect the development of testes in multiple pathways. Furthermore, several hub genes that are regulated by non-CpG methylation during testicular development—such as VEGFA, PECAM1, and FZD7—were also identified. We also found that the relative expression of FZD7 was downregulated by the zebularine-induced demethylation of the first exon of FZD7. This regulatory relationship was consistent with the results of the WGBS and RNA-seq analysis. The immature porcine Sertoli cells were transfected with RNAi to mimic the expression patterns of FZD7 during testicular development. The results of the simulation test showed that cell proliferation was significantly impeded and that cell cycle arrest at the G2 phase was caused by the siRNA-induced FZD7 inhibition. We also found that the percentage of early apoptotic Sertoli cells was decreased by transfecting them with the RNAi for FZD7. This indicates that FZD7 is an important factor in linking the proliferation and apoptosis of Sertoli cells. We further demonstrated that Sertoli cells that were treated with the medium collected from apoptotic cells could stimulate proliferation. These findings will contribute to the exploration of the regulatory mechanisms of non-CpG methylation in testicular development and of the relationship between the proliferation and apoptosis of normal somatic cells.

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Section: Discussionmentioning

confidence: 58%

Section: Resultsmentioning

confidence: 99%