This tutorial review describes the fundamental principles and recent advances in developing small molecule-based therapeutics for disease-associated RNAs.

Advances in deep sequencing technologies have facilitated the identification and annotation of thousands of long noncoding RNAs (lncRNAs) across the transcriptome. LncRNAs are documented to play critical housekeeping roles within the cell and are implicated in a wide variety of diseases, including cancer. While studies into lncRNA function in cancer abound, there are limited examples to date of detailed lncRNA structural analyses to enable understanding of structure‐function relationships. Understanding structure‐function relationships would increase our insight into the noncoding transcriptome and yield potential avenues for targeting lncRNAs implicated in disease. The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) has been identified in multiple clinical studies as a predictive biomarker and molecular driver of aggressive prostate cancer. While several protein interactors have been identified for SChLAP1 to date, structural insight into SChLAP1:protein recognition has not yet been explored. We believe that structural analysis of SChLAP1 will assist in designing specific therapeutic strategies to inhibit SChLAP1:protein interactions implicated in prostate cancer. To this end, we performed Selective 2′‐Hydroxyl Acylation analyzed by Primer Extension with Mutational Profiling (SHAPE‐MaP) and dimethyl sulfate (DMS)‐MaP in vitroand in cellulo. This approach yielded the first secondary structure model of SChLAP1, which revealed a complex architecture with a wide variety of secondary structures throughout the length of the transcript. Analyzing our in‐cell probing data with the ΔSHAPE algorithm, we identified protein binding regions within SChLAP1 and mapped them to non‐human primate‐conserved exons within the transcript. Finally, we identified a smaller, highly structured fragment of SChLAP1 that houses multiple putative protein binding sites implicated in prostate cancer. We believe that this region of SChLAP1 is amenable to therapeutic targeting and may be used as a smaller construct for in vitrodevelopment of SChLAP1‐targeting therapeutics. We also believe this fragment may be amenable to 3D biophysical analyses, such as X‐ray crystallography or cryo‐EM, to further enhance structural understanding of SChLAP1:protein complexation. Ongoing work is focused on determining the sufficiency of this fragment for protein recognition and characterizing potential magnesium‐dependent tertiary structures. We believe this work will facilitate the development of specific therapeutic strategies for SChLAP1 and contribute to the growing need of characterizing structure‐function relationships within lncRNAs.

The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and driver of aggressive prostate cancer. Recent work suggests that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or the SChLAP1:SWI/SNF complex. Herein, we report the first secondary structure model of SChLAP1 utilizing SHAPE-MaP both in vitro and in cellulo. Comparison of the in vitro and in cellulo data via ΔSHAPE identified putative protein binding sites within SChLAP1, specifically to evolutionarily conserved exons of the transcript. We also demonstrate that global SChLAP1 secondary structure is sensitive to both purification method and magnesium concentration. Further, we identified a 3'-fragment of SChLAP1 (SChLAP1Frag) that harbors multiple potential protein binding sites and presents a robustly folded secondary structure, supporting a functional role for this region. This work lays the foundation for future efforts in selective targeting and disruption of the SChLAP1:protein interface and the development of new therapeutic avenues in prostate cancer treatment.