Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Individual Selection and Tissue Collection
2.2. Animal Experimental Design
2.3. DNA Isolation and WGBS
2.4. Data Filtering and Identification of Methylated Cytosines
2.5. Identification and Distribution of Methylated C Sites
2.6. Horizontal Distribution of Methylation in Functional Areas
2.7. Identification of Differentially Methylated Regions (DMRs) and Functional Enrichment Analysis
3. Results
3.1. Sequencing Data Statistics
3.2. Identification of Methylated C Sites and Their Distribution
3.3. Cluster Analysis between Samples
3.4. Distribution of Methylation Levels in Functional Regions of the Genome
3.5. DMR Detection
3.6. Identification of DMGs and Functional Enrichment Analysis
3.7. The Conjoint Analysis of Differential Expression Genes (DEGs) and DMGs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Tissue | DMGs | Trends in Methylation Level |
---|---|---|
hypothalamus | CD2AP, CERK, FBXW11, ROS1, UNC13B, YAP1 | |
hypothalamus | ABLIM2, ENSGALG00000033770, FSD1, HOXA1, NUMB, SLC7A11 | |
ovary | CD2AP, CPXM1, KCNK13 | |
ovary | ENSGALG00000053295 |
Tissues | Groups | Genes | Transcriptional Level | Methylation State | Gene Function |
---|---|---|---|---|---|
Ovary | 1-vs.-2 | PRIMA1 | −1.518 | hypo | proline-rich membrane anchor 1 |
Ovary | 1-vs.-2 | DSTYK | −1.001 | hyper | dual serine/threonine and tyrosine protein kinase |
Ovary | 2-vs.-3 | NKTR | −1.083 | hyper | natural killer cell triggering receptor |
Ovary | 2-vs.-3 | DOCK4 | −1.196 | hypo | dedicator of cytokinesis 4 |
Ovary | 3-vs.-5 | RPS15 | −1.680 | hypo | ribosomal protein S15 |
Ovary | 3-vs.-5 | SMOC1 | −1.709 | hyper | SPARC-related modular calcium binding 1 |
Hypothalamus | 3-vs.-5 | SCAMP3 | −1.062 | hyper | secretory carrier membrane protein 3 |
Hypothalamus | 3-vs.-5 | ATOH8 | −1.050 | hyper | atonal bHLH transcription factor 8 |
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Zhang, T.; Li, C.; Deng, J.; Jia, Y.; Qu, L.; Ning, Z. Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals 2023, 13, 1012. https://doi.org/10.3390/ani13061012
Zhang T, Li C, Deng J, Jia Y, Qu L, Ning Z. Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals. 2023; 13(6):1012. https://doi.org/10.3390/ani13061012
Chicago/Turabian StyleZhang, Tongyu, Chengfeng Li, Jianwen Deng, Yaxiong Jia, Lujiang Qu, and Zhonghua Ning. 2023. "Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting" Animals 13, no. 6: 1012. https://doi.org/10.3390/ani13061012
APA StyleZhang, T., Li, C., Deng, J., Jia, Y., Qu, L., & Ning, Z. (2023). Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals, 13(6), 1012. https://doi.org/10.3390/ani13061012