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.

The noncoding RNA (ncRNA) revolution has revealed myriad RNA species that play critical roles at all stages of life, including developmental biology and disease progression. For example, two long ncRNAs (lncRNA), Metastasis Associated Lung Adenocarcinoma Transcript‐1 (MALAT1; ~6.7 kb) and Second Chromosome Locus Associated with Prostate‐1 (SChLAP1; ~1.5 kb), are basally expressed in normal prostate tissue but are dysregulated in prostate cancer. MALAT1 acts in trans at nuclear speckles during mRNA post‐transcriptional processing while SChLAP1 acts in cis to influence oncogenic gene expression. There is compelling evidence that the 3′‐end of MALAT1 is a triple helix structure that acts as a molecular knot, driving transcript accumulation in cancer cells and furthering its metastatic potential, but we currently lack any biophysical data detailing the relationship between SChLAP1 structure and function. In general, the relationship among lncRNA structure, dynamics, and function is not well understood; for example, even with high‐resolution structures of the MALAT1 triple helix, questions remain regarding the role of intrinsic dynamics in transcript stability or protein binding. As lncRNA represent an underexplored therapeutic avenue, this work aims to investigate the role of lncRNA structure and dynamics in driving prostate cancer metastasis. Current work includes: 1) Understanding the role of the MALAT1 3′‐end triple helix structure and dynamics in global transcript stability and 2) Conducting the first biophysical analyses of SChLAP1 and identifying structural elements that are critical to metastasis. For the MALAT1 project, we have performed chemical probing experiments using both SHAPE‐ and DMS‐MaP chemical probing on the MALAT1 triple helix and 5′‐end extensions, revealing different conformations of the triple helix region. Additionally, we have performed exonuclease degradation assays on the triple helix and 5′‐end extensions in triplex de/stabilizing buffer conditions, showing that transcript stability is indeed tied to triple helix structural dynamic. For the SChLAP1 project, we have determined the first secondary structure model of full‐length SChLAP1 and have data supporting the formation of independent folding domains that when deleted from the full‐length transcript lower the invasive phenotype of prostate cells. We are currently working to investigate the tertiary structure of SChLAP1 and identify structure ensembles. Future work aims to design novel in‐cell mutational studies to identify regions of SChLAP1 that are critical for driving cell migration and invasion, two hallmarks of aggressive prostate cancer. This work will deepen our current understanding of the lncRNA MALAT1 triple helix dynamics in driving prostate cancer metastasis and provide the first biophysical and biochemical assessment of the lncRNA SChLAP1. Through this pursuit, we will provide the basis for assessing novel lncRNA structure‐function relationships and therapeutically targeting lncRNA in cancer. Support or Funding Information E...