Sunday, May 11, 2025
5/11/2025
Identifying and characterizing translation of circular RNAs using high-throughput sequencing data - Title: Identifying and characterizing translation of circular RNAs using high-throughput sequencing data Project Description The purpose of this research is to improve our understanding of a recently discovered circular form of RNA (circular RNA or circRNA) using high-throughput sequencing data to identify and characterize the translation of these structures over a variety of contexts. Over the past two decades, studies have discovered a special form of alternative splicing (AS) that produces a circular form of RNA. This stands in contrast to normal AS which produces a linear form of RNA. Although these circRNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on the regulatory role of circRNAs with the assumption that circRNAs are non-coding. As non-coding RNAs, they may regulate mRNA transcription, tumor initiation, and translation by sponging miRs and RNA-binding proteins (RBPs). In addition to these regulatory roles of circRNAs, however, recent studies have provided strong evidence for their translation. The translation of circRNAs is expected to have an important role in promoting cancer cell growth and activating molecular pathways related to cancer development. In some cases, including our preliminary bioinformatics studies, translation of circRNAs is shown to be efficiently driven by an internal ribosomal entry site (IRES). The development of a computational tool for identifying and characterizing translation of circRNAs using high-throughput sequencing and IRES will increase identifiable proteins translated from circRNAs. In turn, it will have a substantial impact on helping researchers understand the functional role of proteins derived from circRNAs. One of the major application of RNA sequencing (RNA-seq), a powerful technology for analysis of eukaryotic transcriptomes, coupled with ribosome profiling (Ribo-seq) is to find evidence for the translation of novel (or unannotated) mRNA transcripts. Since circRNAs are novel transcripts, RNA-seq provides a perfect platform for genome-wide detection of circRNAs while Ribo-seq provide evidence for the translation of circRNAs. Our own preliminary result from rat brain RNA-seq and rat liver Ribo-seq data has identified 3 circRNAs with evidence of translation. Guided by these data, the current proposal will (Aim 1) develop a novel computational method for identifying and characterizing translation of circRNAs by coupling RNA-seq and Ribo-seq data, and (Aim 2) develop a new web resource for aggregating, cataloging, and visualizing translational information of circRNAs derived from publicly available RNA-seq and Ribo-seq datasets. This proposal will accomplish the objectives of the R15 AREA grant in: (i) supporting meritorious research; (ii) strengthening the research environment of non-research intensive institutions; and, (iii) engaging undergraduate/graduate students in bioinformatics research. The proposed work would act as a foundation for the applicant to establish a program of research aimed at facilitating translated circRNA studies using high-throughput sequencing data. In turn, this would provide researchers with critical information regarding translated circRNAs in existing high-throughput sequencing datasets. Finally, the proposed research will be used as a vehicle to engage undergraduates in multi-disciplinary bioinformatics research and better enable students from Kentucky, a traditionally underrepresented state in bioinformatics, to successfully participate in advanced biomedical research.
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