AI Article Synopsis
- Environmental factors play a role in the development of cleft palate (CP), prompting the need to identify methylated genes during secondary palate development for a deeper genetic-environmental understanding.
- The study utilized genomic DNA from developing palate tissues to pinpoint methylated genes, employing techniques like Selective Enrichment of Methylated DNA (SEMD) and analyzing data through Ringo, validating findings with pyrosequencing and quantitative real-time PCR.
- Results showed a significant number of methylated genes (5577), with most being consistently methylated across gestational days and predominantly located in gene bodies, highlighting important pathways like cadherin, Wnt signaling, and proteoglycan synthesis that might influence gene expression during palate development.
Article Abstract
Background: Environmental factors contribute to the etiology of cleft palate (CP). Identification of genes that are methylated during development of the secondary palate will contribute to a better understanding of the gene-environment link contributing to CP.
Methods: Genomic DNA fragments from secondary palate tissue from gestational days (GDs) 12 to 14 were subjected to Selective Enrichment of Methylated DNA (SEMD) and used to probe NimbleGen 2.1M mouse promoter arrays. Input (control) and SEMD samples were labeled with Cy3 and Cy5, respectively, and used for array hybridization (three arrays per GD). Data were analyzed using the Bioconductor package Ringo. Gene methylation was verified by pyrosequencing analysis and expression by quantitative real-time PCR.
Results: A total of 5577 methylated genes were identified during palate development: (1) 74% of genes were methylated on all three GDs; (2) CpG islands accounted for only 30% of methylated regions of interest (MRIs); (3) location of MRIs was more often observed in gene bodies (73%) than in promoters; (4) evaluation of MRIs on GDs 12-14 revealed no significant differentially methylated regions; (5) DAVID analysis of MRIs revealed that the cadherin and Wnt signaling pathways, as well as pathways involved in proteoglycan synthesis, were significantly enriched for methylated genes.
Conclusions: Our prior studies identified differentially expressed mRNAs and microRNAs in the developing palate. The current study complements these studies by identifying genes whose expression may be altered as a result of DNA methylation.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776452 | PMC |
| http://dx.doi.org/10.1002/bdra.23126 | DOI Listing |
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