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Abstract Circular RNAs are associated with numerous diseases and recent evidence shows that they can be translated into proteins after undergoing RNA modification. Circular RNAs differ from their ‘linear’ mRNA counterparts in their backsplice site, allowing selective targeting using RNA interference, which however limits the options to place the siRNA. We tested all possible siRNAs against the backsplice site of the circTau 12->7 RNA after it was subjected to adenosine to inosine RNA editing, a modification that promotes translation of the circRNA. Most siRNAs reduced the circRNA and protein abundance, which however did not correlate. We identified an siRNA with an IC50 of 750 pmol efficacy on protein expression. This circRNA fulfilled six of the eight criteria for siRNAs targeting mRNAs. Thus, modified circRNAs expressing protein can be targeted with siRNAs, but their optimal sequence needs to be determined empirically.
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Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus
Abstract Circular RNAs (circRNAs) are covalently closed single‐stranded RNAs, generated through a back‐splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs fromLotus japonicusleaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified inL. japonicusto other plant species and showed conservation of high‐confidence circRNA‐expressing genes. This is the first identification ofL. japonicuscircRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA inL. japonicus.
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- Award ID(s):
- 1828820
- PAR ID:
- 10644368
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- The Plant Genome
- Volume:
- 17
- Issue:
- 1
- ISSN:
- 1940-3372
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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