A Genome-Scale Analysis of Alternative Splicing Regulation by Splicing Factors in C. elegans

Alternative splicing (AS) is a key mechanism that contributes to the high level of complexity present within metazoan proteomes. This process is highly regulated and important for the development for any animal. With advances in high-throughput technologies, our knowledge of the many AS events that occur in the cell has rapidly increased. However, for many of these events, it is still not known which splicing factors (SF) are involved, and how they regulate splicing outcomes. Here, I use a genomic approach in the nematode C. elegans to study how SFs govern AS events during development. Specifically, for this thesis, I focus on four SFs – ASD-1, FOX-1, EXC-7 and MEC-8. In the first data chapter, I use RNA sequencing, RNA-binding preferences and conservation information to identify likely direct targets of these SFs. I find that AS regulation by these SFs is often combinatorial and converges upon genes with neuronal and cytoskeletal functions. I further show that loss of these SFs can lead to synergistic defects in the neuromuscular system. Many of these co-regulated AS events are also developmentally regulated, suggesting a crucial role in development. In the second data chapter, I then focus on a subset of MEC-8 targets to provide a more detailed view of splicing regulation. I find that MEC-8 regulates the developmental AS transitions in multiple transcripts encoding components of the fibrous organelle – a complex crucial for maintaining structural integrity in the worm. Differential mec-8 expression during development likely contributes to the dynamic regulation of these AS events in a cell- and developmental-stage specific manner. Finally, I find that these AS patterns can vary among C. elegans natural isolates and differential splicing is associated with differences in mec-8 expression. These data suggest that the study of natural variation in AS regulation can provide insight into the regulation of splicing regulatory pathways.

Department dc:contributor.department

Molecular and Medical Genetics

Year dc:date.issued

2018

Author dc:creator

• Tan, June Hui Jun

Advisor dc:contributor.advisor

• Fraser, Andrew G

• Alternative splicing
• C. elegans
• Genetics
• Genomics

Handle dc:identifier.uri

http://hdl.handle.net/1807/91985

OAI identifier oai:identifier

oai:utoronto.scholaris.ca:1807/91985