Role of Retrotransposons as a Major Source of Intra- and Inter-Individual Epigenetic Variations in the Mammalian Genome
Transcription of retrotransposons is usually repressed by DNA methylation, but a few elements partially escape this repression mechanism. I used two approaches as my dissertation study to identify unmethylated intracisternal A-particles (IAPs) and also to understand why some of IAPs escape DNA methylation-mediated repression. Firstly, I sought to catalog the retrotransposons (LTRs and LINEs only) in the mouse genome known as ‘epialleles’ which escape the repression variably even in individuals with an identical genome sequence. Using bioinformatic approaches, 143 candidate epialleles were first identified based on their promoter activity and association with active histone modification marks. Detailed methylation analyses suggested that a subset of these elements showed variable levels of DNA methylation inter-individually, revealing their stochastic nature (metastability) of DNA methylation. The analyses also identified two opposite patterns of DNA methylation, progressive gaining versus losing, during development. qRT-PCR analyses demonstrated that the expression levels of these elements are indeed variable among the individual mice, suggesting functional consequences on their associated endogenous genes. Next, for a large scale individual element or loci-based methylation analyses of the candidate epiallele IAPLTRs and other repeat elements, we proposed and validated a novel high-throughput targeted repeat element bisulfite sequencing (HT-TREBS) technique. We obtained CpG methylation data of 5135 loci of five IAPLTR subtypes in three different tissues of four 1-week-old mouse littermates. An average of 52,000 CpG positions per sample with average sequencing depth of 117x was reported. More than 80% of the targeted subtype loci and less than 15% of the non-targeted subtype loci of IAPLTRs have been covered by this technique. Data analyses revealed that 2% of the IAPLTR loci have less than 80% average CpG methylation with no genomic position preference and the majority of these loci are of the IAPLTR2 and IAPLTR2a subtypes. Further analyses also revealed extensive tissue-specific, individual-specific (epialleles), stochastic (random), and even sex-specific CpG methylation variations in the IAPLTR loci. Overall, our data confirmed the presence of many new retrotransposon-derived epialleles and other epigenetic variations. Our efficient and robust technique HT-TREBS also provided a lot of novel insight in to the epigenome of the IAPLTR repeat elements.
DNA methylation, IAPLTR, epigenetics, inter-individual variation, intra-individual variation, retrotransposon, epiallele, metastable epiallele, repeat element bisulfite sequencing, active histone modification
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