PhD Proposal Seminar – Sanjana Bhatnagar (Calarco Lab)

Alternative splicing (AS) is a major contributor of cellular complexity and its regulation is highly variable and context dependent. Many studies have focused on investigating the major regulators of AS, cis-elements and trans-factors, by learning predictive models on native sequences and through in vitro studies or cell-based screens. However, investigating the roles of a multitude of these factors in a more systematic manner in vivo is challenging and remains an understudied area. The goal of my thesis is to develop a system to investigate different cis-elements and trans-factors in parallel and in different contexts in vivo. I propose employing a parallel reporter assay (PRA) in Caenorhabditis elegans, an excellent model organism with complex AS regulation. I will employ this approach to screen thousands of random sequences and identify cis-elements regulating AS in tissues and in individual neuron classes. I hypothesize that through this approach I will be able to identify sequence features and trans-factors associated with tissue- and single neuron-biased splicing patterns. Together, this work will provide insight into the mechanisms governing tissue and cell-specific splicing patterns in vivo.

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