UNDERSTANDING TRANSCRIPTIONAL RESPONSES TO ENVIRONMENTAL AND DEVELOPMENTAL CUES IN MODEL ORGANISMS USING FULL-LENGTH SINGLE CELL RNA-SEQ

Recent advancements in single-cell RNA sequencing have revolutionized our understanding of gene expression regulation under various biological contexts, providing higher resolution and system-level insights compared to traditional bulk RNA sequencing methods. In this dissertation, we utilize single cell RNA-seq (scRNA-seq) along with various statistical tools to unveil the stress response and developmental transcriptomic landscape of four model organisms. First, we sequenced yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length single-cell RNA-Seq method. We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions as well as putative regulatory relationships between transcription factors and target genes.
Our results show that a full-length single-cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods. Second, we present a transcriptomic level analysis into the oogenesis of C. elegans hermaphrodites. We dissected a hermaphrodite gonad into seven sections corresponding to the mitotic distal region, the pachytene, the diplotene, the early diakinesis region and the 3 most proximal oocytes, and deeply sequenced the transcriptome of each of them along with that of the fertilized egg using a single-cell RNA-seq protocol. We identified specific gene expression events as well as gene splicing events in finer detail along the oocyte germline and provided novel insights into underlying mechanisms of the oogenesis process. Furthermore, through careful review of relevant research literature coupled with patterns observed in our analysis, we attempt to delineate transcripts that may serve functions in the interaction between the germline and cells of the somatic gonad. These results expand our knowledge of the transcriptomic space of the C. elegans germline and lay a foundation on which future studies of the germline can be based upon. Lastly, we profiled mature oocytes and 1-cell zygotes of mice and rats to uncover elusive transcriptomic dynamics in the maternal to zygote transition. We confirm the existence of early gene expression in the mouse zygotic while revealing a similar chain of events occurring in the rat zygote. We observe an increase in nascent transcription in both species. Moreover, we find subtle but pervasive signals of differential splicing of genes related to key early zygotic activities occurring in both species. Meanwhile, we find distinct profiles of alternative polyadenylation between zygotes and oocytes in both species, specifically in genes related to major processes within the zygote. Finally, although a more dynamic transcriptomic landscape exists in the mice zygote, the rat zygote also displays similar transcriptomic features, suggesting that minor zygotic activation in rat occurs earlier than originally thought.