Battle of the X’s: Utilizing Mitochondrial Phylogenies to Investigate X-Chromosome Imprinting
Isaac Walker
Department of Biology
Faculty Supervisor: Scott Roy
Genomic imprinting is an epigenetic mechanism where one allele is expressed, and the other is silenced. It’s hypothesized that imprinting evolved from differing parental interests in resource allocation for their offspring. Imprinting occurs pre-fertilization, and has significant implications for development, growth, and disease. In mammals, this phenomenon has been well documented in autosomes, but very little investigation has been done in the X-Chromosome. Each cell in female (XX) mammals expresses only one X, allowing us to study imprinting by comparing cells expressing different Xs. To assess X chromosome expression in single cell RNA-seq data (scRNA), a method for building cell phylogenies is needed. Mitochondrial data were extracted from the scRNA data and divided per cell. These per cell files were analyzed using samtools and custom scripts, and diversity metrics were calculated, quantifying the genetic diversity. Finally, a distance matrix was created based on these cells diversity profiles. Then X-Chromosome data was extracted in a similar way, and analyzed separately. These two matrices were then compared, to identify correlations in the data, which allowed us to group cells by which of the two X chromosomes they are expressing, allowing for studying X chromosome imprinting.