In silico comparative genomic analysis of DNA and Histone-Methylation proteins and transcripts across model organisms and Metschnikowia yeasts

Abstract

This thesis investigates if canonical DNA and histone methylation pathways are conserved in the non-conventional yeast genus Metschnikowia, with a partial focus on M. pulcherrima. Using a bioinformatics comparative genomics approach with reference genes and proteins from Homo sapiens, Mus musculus, Drosophila melanogaster and Saccharomyces cerevisiae as BLAST queries against available Metschnikowia genomes. The results showed that classical DNA methylation pathways (DNMT1, DNMT3A, DNMT3B and TET dioxygenases) are largely absent across the genus, indicating that the species do not rely on cytosine methylation-based gene regulation. However, several of the histone methylation and demethylation proteins and protein domains, particularly SET-domain methyltransferases and JmjC-domain demethylases showed some conservation. These hits were strongest and most consistent in M. bicuspidata, suggesting that chromatin-based regulatory mechanisms are preserved in this lineage. These findings highlight significant epigenetic divergence within the Metschnikowia genus, and supporting the conclusion that M. pulcherrima and related species most likely rely on an alternative non-DNA-methylation pathway for transcription control. The study emphasizes the need for further functional and genomic research into the chromatin biology of non-conventional yeasts.