Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells
Abstract
:1. Introduction
2. Results
2.1. Co-Localization of Transcription Factor Cis-Regulatory Motifs
2.2. Effects of Methylation Changes on the Activity of Transcription Factors
3. Discussion
4. Materials and Methods
4.1. Purification of Bovine Endometrial Epithelial Cells
4.2. Methylation and Gene Expression Data
4.3. Transcription Factor Binding Sites Analyses
4.4. Colocalized Motifs in DMRs
4.5. Analysis of Global Methylation Levels of TFBSs and Expression of Transcription Factors
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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Class | Transcription Factors |
---|---|
Basic helix-loop-helix factors (bHLH) | ARNT, Bhlha15, HES1, AHR, HEY1, HEY2, MYC, MXI1, MYCN, TFE3, MAX, NEUROD2, HIF-1α, USF1, TCFL5, TAL1, TCF3, NEUROG1, TFEB, TCF4, FIGLA |
Homeo-domain factors | POU5F1, MEIS1, HOXC10, HOXC11, HOXC12, HOXC13, ONECUT2, HOXA11, HOXD11, HOXD12, TLX1 |
Basic leucine zipper factors (bZIP) | CREB3, CREB3L1, MAFK, BACH1, BACH2, FOS, NRL, FOSL1, JUN, NRF1 |
C2H2 zinc finger | ZSCAN4, YY1, YY2, ZNF423, CTCF, ZFX, EGR1, EGR2, EGR3 |
STAT domain factors | STAT1, STAT2, STAT3, STAT5A, STAT5B, STAT6 |
Tryptophan clusters | IRF1, IRF2, IRF7, MYB, HLTF |
Nuclear receptors with C4 zinc fingers | NR1H3, RXRA, NR4A2, NR2E1 |
Fork head/Winged helix | FOXB1, FOXA1, FOXJ2, FOXO1 |
Paired box | PAX2, PAX5 |
Basic helix-span-helix factors (bHSH) | TFAP2C |
Runt domain | RUNX3 |
C4 zinc finger-type factors | GATA1 |
Rel homology region (RHR) factors | RELA |
SMAD/NF-1 DNA-binding domain factors | NFIC |
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Jhamat, N.; Guo, Y.; Han, J.; Humblot, P.; Bongcam-Rudloff, E.; Andersson, G.; Niazi, A. Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells. Int. J. Mol. Sci. 2024, 25, 9832. https://doi.org/10.3390/ijms25189832
Jhamat N, Guo Y, Han J, Humblot P, Bongcam-Rudloff E, Andersson G, Niazi A. Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells. International Journal of Molecular Sciences. 2024; 25(18):9832. https://doi.org/10.3390/ijms25189832
Chicago/Turabian StyleJhamat, Naveed, Yongzhi Guo, Jilong Han, Patrice Humblot, Erik Bongcam-Rudloff, Göran Andersson, and Adnan Niazi. 2024. "Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells" International Journal of Molecular Sciences 25, no. 18: 9832. https://doi.org/10.3390/ijms25189832