Structural and Functional Studies of lncRNAs in Gene Activation - Project Summary Over the last two decades, breakthroughs in sequencing technologies have revealed that mammalian genomes encode thousands of long non-coding RNAs (lncRNAs). The numbers of human lncRNAs that are known to be dysregulated in diseases are rising at a rapid pace. Emerging evidence suggests that lncRNAs are critical regulators of fundamental cellular processes and disease progression. Despite their significance as potential biomarkers and therapeutic targets, the molecular mechanisms of lncRNAs remain poorly understood. The primary goal of this research is to elucidate in greater detail the mechanisms by which lncRNAs activate transcription. Many lncRNAs are associated with epigenetic machinery; these include histone-modifying complexes, such as the polycomb repressive complex 2, and nucleosome remodeling complexes, such as the SWI/SNF (SWItch/Sucrose Non-Fermentable) complex. While the RNA-PRC2 interactions are under active investigation, the role of lncRNAs in nucleosome remodeling remains uncharacterized. Here, we seek to understand the function of lncRNAs in SWI/SNF-based gene activation. The SWI/SNF complex is a known tumor suppressor, and its subunits are mutated in various cancers. Recently, lncRNAs have been shown to interact with the SWI/SNF complex in mammals and plants. In this proposal, we will utilize lncTCF7 to investigate the role of lncRNAs in SWI/SNF-based gene activation. Previous studies have shown that lncTCF7 activates Wnt signaling by recruiting the SWI/SNF complex. However, the biochemical and structural basis of these interactions is not established. In preliminary studies, we identified SND1 (Staphylococcal Nuclease and Tudor Domain Containing 1) as the top interaction partner of lncTCF7. SND1 is a transcriptional coactivator, and it is known to associate with the SWI/SNF family. Here, we propose a novel mechanism suggesting that lncTCF7 recruits the SWI/SNF complex indirectly via its interaction with SND1. Further, our RNA chemical probing studies identified structural domains and regions of lncTCF7 conserved across mammalian genomes. We hypothesize that these conserved regions and structured elements play critical roles in recruiting protein partners and activating transcription at specific loci. We will test this hypothesis through the following aims: In Aim 1, we will define the functional role of lncTCF7’s domains. Aim 2 will determine the role of lncTCF7-SND1 interaction in recruiting the SWI/SNF complex and activating transcription. In Aim 3, we will determine the 3D structure of lncTCF7 and the lncTCF7-SND1 complex. Together, these studies will provide biochemical and structural knowledge of lncTCF7’s molecular function and expand our understanding of how lncRNAs regulate gene transcription and contribute to disease states.
