Developmental Regulation of Gene Expression by Long Undecoded Transcript Isoforms

PROJECT SUMMARY Dynamic gene expression programs drive essential biological processes including cellular differentiation and stress response pathways. During these processes, cells must simultaneously activate and repress distinct clusters of genes to facilitate the necessary shift in proteome synthesis. How gene repression is achieved

amidst widespread transcriptional activation is not well understood. My lab has recently discovered a regulatory mechanism in budding yeast meiosis that achieves such coordination. Central to this mechanism is the transcription factor-driven expression of an alternative mRNA isoform called LUTI (Long Undecoded

Transcript Isoform) from a distal gene promoter. This mRNA cannot produce functional protein due to competitive upstream open reading frames (uORFs) in its extended 5' leader. Instead, its transcription serves to repress the canonical mRNA transcription in cis through chromatin modifications, ultimately leading to

inhibition of protein synthesis. Therefore, transcription of these mRNAs, despite carrying a full coding region, can directly cause gene repression. Consequently, a single transcription factor can synchronously activate and repress protein synthesis for distinct sets of genes, depending whether it binds to a canonical or a LUTI

promoter, respectively. Furthermore, this mechanism is tunable and reversible, making it ideal for fluid cell state transitions that rely on dynamic changes in gene expression. The LUTI-based mechanism is neither limited to meiosis nor restricted to budding yeast, as it occurs during the unfolded protein response and is conserved in human cells. Importantly, the two essential branches

of this regulation are both associated with human disease. First, misregulation of alternative transcription start sites is widespread across multiple cancers. Second, disruption of uORF expression is linked to a variety of disorders ranging from gonadal dysgenesis to melanoma. Therefore, dissecting the mechanism and biological

scope of LUTI-based regulation is critical for our understanding of how cells control their gene expression programs, and how mistakes in this process can lead to pathological states. This proposal seeks to address fundamental questions regarding the mechanism and function of LUTI-based regulation in yeast and human

cells. Experiments proposed in aim 1 will investigate how transcriptional repression is achieved by activation of LUTI promoters during meiosis and the unfolded protein response, where LUTIs are pervasively expressed. Experiments proposed in aim 2 will elucidate how the LUTI-based regulation is integrated into larger signaling

networks to ensure precise and robust cell state transitions. Finally, experiments proposed in aim 3 will determine the evolutionarily conserved aspects of LUTI-based regulation and uncover the biological roles of LUTIs during human embryonic stem cell differentiation. The combination of studies described in this proposal

will illuminate how cells dynamically control their gene expression programs with transcription factor-driven waves of coordinated gene activation and repression, not anticipated prior to our discovery of LUTIs.