Study of the Effect of Epigenetic Control on Cell Fate through Diverse Mechanisms in Multiple Organisms
Sathe, Adwait Amod
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Epigenetic factors are responsible for regulating cell fate in different model systems in diverse ways. In this study I present two epigenetic factors which play a role in the development of cell types. CpG island DNA hypermethylation on gene promoters is a well studied epigenetic factor. It affects the gene expression either through direct gene inhibition or as a marker for a phenotype. Aberrant DNA methylation can act as initial transformation indicators, bio-markers or in some cases even drug targets for cancer cells. In this dissertation I describe the discovery of a gene promoter, SCT (secretin) which is hypermethylated in more than 15 tumor types including Non-small Cell Lung Cancer and Squamous cell carcinoma. It is almost completely unmethylated in cancer matched normal tissue as well as ~1000 non-cancerous tissues across > 30 organ types. The lung cancer samples could thus be distinguished from the non-malignant tissues as their area under the curve,(AUC) is 0.98 for over 801 samples. This was found using statistical analysis of 450k methylation array data in The Cancer Genome Atlas (TCGA), GEO, ENCODE and other large public databases. After lab validation using quantitative Methylation Specific Polymerase Chain Reaction (qMSP), it was proved that SCT is a hallmark bio-marker for Non small Cell Lung and other malignant tumors, is infrequent in less aggressive malignant tumors (including lung carcinoids), and appears very early in tumorigenesis i.e., carcinoma in situ stage. In early embryonic development transcription is largely quiescent and translation as well as the chromatin structure are controlled by epigenetic factors. In mammals, DNA and histone methylation act as major epigenetic regulators of embryo development. But in organisms lacking CpG island methylation and a limited set of histone modifications like C. Elegans, other factors like RNA interference and short non-coding RNAs play a major role. Small non-coding RNAs like piRNA, miRNA and siRNA affect gene expression by binding to specific sites on their target mRNAs leading to their degradation. Computational analysis of Next Generation Sequencing data, shows how these small RNAs affect the degradation of specific maternal RNAs in Maternal to Zygotic transition (MZT) in C. elegans embryo development. This mechanism of epigenetic control is also seen in most of the animals like drosophila, mice and humans. I show how a specific piRNA 21ur-15753 in addition to the 26G endo siRNAs can trigger the production of small RNAs from a locus involved in somatic cell fate specification called very early transcript-5 or vet-5. These are responsible in degrading a specific set of RNAs inherited from the mother which contain a relatively higher proportion of the AU rich element pattern 'AUUUAU' responsible for RNA degradation.