Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development
Proper placental development is crucial for the conceptus to grow and survive, because the placenta is responsible for transporting nutrients and oxygen from the pregnant female to the developing fetus. However, the processes of placental morphogenesis and fold formation remain to be fully elucidate...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/6/5169 |
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| author | Baohua Tan Chen Zhou Xupeng Zang Xinming Zhao Liyao Xiao Jiekang Zeng Linjun Hong Zhenfang Wu Ting Gu |
| author_facet | Baohua Tan Chen Zhou Xupeng Zang Xinming Zhao Liyao Xiao Jiekang Zeng Linjun Hong Zhenfang Wu Ting Gu |
| author_sort | Baohua Tan |
| collection | DOAJ |
| description | Proper placental development is crucial for the conceptus to grow and survive, because the placenta is responsible for transporting nutrients and oxygen from the pregnant female to the developing fetus. However, the processes of placental morphogenesis and fold formation remain to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to produce a global map of DNA methylation and gene expression changes in placentas from Tibetan pig fetuses 21, 28, and 35 days post-coitus. Substantial changes in morphology and histological structures at the uterine–placental interface were revealed via hematoxylin–eosin staining. Transcriptome analysis identified 3959 differentially expressed genes (DEGs) and revealed the key transcriptional properties in three stages. The DNA methylation level in the gene promoter was negatively correlated with gene expression. We identified a set of differentially methylated regions associated with placental developmental genes and transcription factors. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of 699 DEGs that were functionally enriched in cell adhesion and migration, extracellular matrix remodeling, and angiogenesis. Our analysis provides a valuable resource for understanding the mechanisms of DNA methylation in placental development. The methylation status of different genomic regions plays a key role in establishing transcriptional patterns from placental morphogenesis to fold formation. |
| first_indexed | 2024-03-11T06:27:15Z |
| format | Article |
| id | doaj.art-9ac7ed18bf084bd489a51bfc9c8b4afa |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T06:27:15Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-9ac7ed18bf084bd489a51bfc9c8b4afa2023-11-17T11:30:03ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-03-01246516910.3390/ijms24065169Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental DevelopmentBaohua Tan0Chen Zhou1Xupeng Zang2Xinming Zhao3Liyao Xiao4Jiekang Zeng5Linjun Hong6Zhenfang Wu7Ting Gu8National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, ChinaProper placental development is crucial for the conceptus to grow and survive, because the placenta is responsible for transporting nutrients and oxygen from the pregnant female to the developing fetus. However, the processes of placental morphogenesis and fold formation remain to be fully elucidated. In this study, we used whole-genome bisulfite sequencing and RNA sequencing to produce a global map of DNA methylation and gene expression changes in placentas from Tibetan pig fetuses 21, 28, and 35 days post-coitus. Substantial changes in morphology and histological structures at the uterine–placental interface were revealed via hematoxylin–eosin staining. Transcriptome analysis identified 3959 differentially expressed genes (DEGs) and revealed the key transcriptional properties in three stages. The DNA methylation level in the gene promoter was negatively correlated with gene expression. We identified a set of differentially methylated regions associated with placental developmental genes and transcription factors. The decrease in DNA methylation level in the promoter was associated with the transcriptional activation of 699 DEGs that were functionally enriched in cell adhesion and migration, extracellular matrix remodeling, and angiogenesis. Our analysis provides a valuable resource for understanding the mechanisms of DNA methylation in placental development. The methylation status of different genomic regions plays a key role in establishing transcriptional patterns from placental morphogenesis to fold formation.https://www.mdpi.com/1422-0067/24/6/5169DNA methylationpigplacental developmenttranscriptome |
| spellingShingle | Baohua Tan Chen Zhou Xupeng Zang Xinming Zhao Liyao Xiao Jiekang Zeng Linjun Hong Zhenfang Wu Ting Gu Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development International Journal of Molecular Sciences DNA methylation pig placental development transcriptome |
| title | Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development |
| title_full | Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development |
| title_fullStr | Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development |
| title_full_unstemmed | Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development |
| title_short | Integrated Analysis of DNA Methylation and Gene Expression in Porcine Placental Development |
| title_sort | integrated analysis of dna methylation and gene expression in porcine placental development |
| topic | DNA methylation pig placental development transcriptome |
| url | https://www.mdpi.com/1422-0067/24/6/5169 |
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