CLAP-seq: An Aptamer-Based Platform for Transcriptome-Wide Mapping of RNA Modifications

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Project Summary/Abstract Beginning in the 1950s, more than 100 types of posttranscriptional modifications have been identified in cellular RNA. Today, the study of RNA post-transcriptional modifications – known as epitranscriptomics – is a rapidly developing field, which promises to greatly enhance our understanding of human health and disease. Despite the profound implications already assigned to many RNA modifications, their precise functions remain poorly understood. This can be attributed to the lack of sensitive and robust sequencing technologies to detect these epitranscriptomics marks in a transcriptome-wide manner. A key bottleneck is the lack of sensitive and specific enrichment techniques (affinity- or reactivity-based) for RNA molecules containing these modifications. The proposed research takes direct aim at this critical deficit using the aptamer approach, employing in vitro selection methods to identify nucleic acid molecules that bind chemically modified RNAs. These aptamers are unique in that they are comprised of L-(deoxy)ribose-based nucleic acids (L-DNA and L-RNA), which are mirror images (enantiomers) of natural D-nucleotides. L-Aptamers, which are completely orthogonal to natural biology, are extremely well suited for binding RNA targets. Therefore, in vitro selection will be used to isolate novel L- aptamers capable of binding chemically modified mononucleotides, which will enable selective capture of RNA molecules containing the same modified residue. These L-aptamers will then be used in Cross-Linking- Aptamer Pull-down and sequencing (CLAP-seq), the first transcriptome-wide profiling technology employing aptamer-based RNA enrichment prior to next-generation sequencing. CLAP-seq not only promises to open a general and robust route towards transcriptome-wide profiling of the growing list of RNA modifications, but also promises to reinforce our current view of the epitranscriptome. Accordingly, the development of CLAP-seq will have a profound impact on the field of epitranscriptomics, which is well aligned with the mission of the NICHD and the goal of this FOA: to promote research into the role of RNA chemical modifications in development and related disease.