Experimental analysis of the genomic determinants of tissue-specific splicing
Shourya Giri, Aaryan Chhabra, Sridevi Sureshkumar and Sureshkumar Balasubramanian*
School of Biological Sciences, Monash University, VIC 3800, Australia
*Correspondence: mb.suresh@monash.edu
Differential splicing is fundamental for generating transcript diversity in multicellular organisms, enabling fine-tuned gene expression and the production of proteins with specialized functions. Tissue-specific splicing, a major subtype of context-specific differential splicing, involves the preferential usage of distinct splice sites in different tissue types with functional diversification. Classic models describe splice site selection through canonical cis-elements (5′SS, 3′SS, BPS, PPT), flanking enhancer/silencer motifs, hexamer rankings, RNA secondary structure, and recruitment of RNA-binding proteins (RBPs). However, in many tissue-specific cases the local genomic features are essentially identical between tissues, yet the splice site choice diverges dramatically. This highlights a fundamental limitation that the currently known set of regulatory elements cannot fully explain tissue-specific splicing. While several examples for RBPs that are expressed in a tissue-specific manner exist, there is no systematic analysis of genomic determinants that govern tissue-specific splicing. More recently, we have uncovered genomic determinants of tissue-specific splicing in a million GWAS study (Chhabra and Balasubramanian, personal communication). Here we test whether these genomic determinants indeed govern tissue-specific splicing using CRISPR-based experimental approaches. I will present our latest results from this ongoing project. Our work will advance mechanistic understanding of splice site regulation and generate a framework for a rational, context-dependent modulation of gene expression, with direct relevance to therapeutic engineering of splicing in disease.