Transcriptomic studies on the production and cytosolic fate of alternative isoforms in mammalian cells
The vast majority of human genes are now known to (at least occasionally) give rise to multiple alternative isoforms. Alternative isoforms of the same gene are now known to have the potential to exhibit vast differences in RNA localization, stability, translational efficiency, and even function of their encoded protein products. Despite more than four decades of research in this area, however, the extent to which the properties of alternative isoforms are known remains minimal. The advent of next-generation sequencing technologies heralded a new era in the study of alternative isoforms. The increasing power and accessibility of technologies these techniques has allowed them to play a substantial role in pulling back the curtains and enable thorough cataloging efforts. Beyond the ability to simply identify and quantify transcripts in a high-throughput fashion across a host of different tissue and cell types, next-generation sequencing has enabled the creation of technologies that allow the measurement of (proxies of) translational efficiency and RNA binding protein binding profiles. In this work we describe our efforts in these directions. First, we introduce software we developed for the identification, quantification, and contextual elaboration of events that distinguish alternative isoforms. We also highlight two efforts towards leveraging and increasing the power of next-generation sequencing to illuminate the properties of alternative isoforms: 1) the application and characterization of Frac-seq applied to early neurodifferentiation, and its implications for studying isoform-specific translation efficiency and nonsense-mediated decay, and 2) characterization of RNA-seq applied to in vitro models of human and close primate brain development, and its implications for alternative event dynamics through differentiation.