Abstract 1411 Structural Spatial Transcriptomics: Novel "Omics" Technology

The canonical right-handed helix, i.e., B-DNA, is the dominant form of DNA in vivo. Nucleic acids can form a variety of totally different non-canonical structures such as Z-DNA, Z-RNA, cruciform DNA, triplex DNA, G4-quadruplex DNA, i-motif quadruplex DNA, and RNA G-quadruplexes. Canonical nucleic acids are found in the forms of right-handed B-DNA and right-handed A-RNA. The formation of these non-canonical, alternative (e.g., Z-DNA) and multistranded (G4-DNA) DNA and RNA structures and their stabilities depends on different environmental factors, e.g., DNA supercoiling, ions and nucleic acid binding proteins. Conventional spatial transcriptomics determines the number of transcripts of a single gene at distinct spatial locations in a tissue. We are presenting data on a novel "omics" method, i.e., Structural Spatial Transcriptomics (SST) (also referred to as Structural Spatial Nucleic Acid Transcriptomics) (SSNAT). This novel approach emphasizes the secondary, tertiary and quaternary structures of RNA molecules. This technology allows for high sensitivity, which accurately identifies different RNA structures. Little is known about the effects of RNA structures on transcription. SST examines how canonical and alternative RNA structures affect transcriptional processes. This technology allows for the identification of right-handed A-RNA and left-handed Z-RNA during expression profiling. It also allows for characterization of expression levels of different structures of RNAs in a given cell population. Left-handed Z-RNA is a higher-energy, conformation of RNA, with little known about its function. SST will help find the regulatory role of this passing form of RNA. Both anti-Z-RNA and anti-A-RNA antibodies, along with labelled RNA probes, are employed. Conjugated secondary antibodies were used to determine specific locations of antibody binding. An noteworthy aspect of Z-RNA is the presence of the sugar 2′-hydroxy groups of guanosine residues displayed on the surface of the helix, which is important for protein binding. SST characterizes the effect of RNA structures on gene expression and will help to explain the process of transcription more fully. Additionally, it determines the relationship between DNA structures and RNA structures in regulating transcription. Defining the spatial distribution of RNA molecules, based on their structures, permits the investigator to better understand the cellular heterogeneity in cell lines, FFPE tissue sections, as well as establish the subcellular distribution of transcripts in a variety of different settings. SST will allow researchers to identify spatial interactions, specific RNA biomarkers, and cancer transcriptomes in their natural tissue architecture, helping investigators to identify potential RNA structure-based drug targets. Research supported in part by an NYIT ISRC grant.