Two of the most critical stages in early development occur during the maturation of oocytes and during the first lineage specification during morula-to-blastocyst transition. The accurate regulation of the transcriptome during these essential events is necessary for the development of a healthy embryo. This thesis presents the culmination of custom pipelines developed to produce three meta-analyses: 1) transcriptome changes during oocyte maturation across four mammalian species (human, rhesus monkey, cow, and mouse), 2) predictive modeling of RNA binding proteins and microRNAs binding to the 3' UTR, impacting stability during oocyte maturation across four mammalian species (human, rhesus monkey, cow, and mouse), and 3) transcriptome changes during the morula-to-blastocyst transition and the establishment of the inner cell mass and trophectoderm across five mammalian species (human, rhesus monkey, cow, pig, and mouse). The results of these studies reveal that there are relatively few individual transcripts regulated commonly across species, while there are greater shared features at the pathway and functional level. This underscores that different species may utilize a different cohort of genes to accomplish a given outcome. Additionally, the pipelines developed for this thesis are highly applicable across many areas of biology.
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