Project 462859

A typical mammalian gene specifying protein synthesis is divided into coding and non-coding segments, referred to as exons and introns, respectively. When genes are transcribed into precursor messenger (pre-m)RNA, the process of splicing joins the exons and excises the introns to produce mature mRNAs that can be translated into proteins. We and others have shown that for more than 90% of human genes, exons are spliced in different combinations to generate different mRNA isoforms. Moreover, for approximately two-thirds of genes, one or more intron can be differentially retained in otherwise mature transcripts. Additional studies from our group and others have defined distinct and biologically important repertoires of alternatively spliced exons and introns that function at different stages of development and that underlie human disease states. However, these studies have primarily focused on the detection of alternatively spliced variants in mixed populations of cells such as intact tissues, whereas relatively little is known about how repertoires of alternatively spliced variants differ between specialized cell types. Moreover, the biological functions of the vast majority of alternatively spliced exons and introns are not known. We propose to harness new RNA profiling and gene editing strategies, together with complementary approaches, to address these questions. Our proposed research will significantly advance knowledge of the functional roles of regulated exons and introns, in the contexts of both normal and diseased states. It will also deliver methods to foster the broader application of exon- and intron-resolution functional genomics among the biomedical research community.