The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs
Open accessAbstract
High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin and functions are largely unknown. Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs. While exoribonuclease treatment is widely used to degrade linear RNAs and enrich circRNAs in RNA samples, it does not efficiently eliminate all linear RNAs. Here, we describe a novel method for the isolation of highly pure circRNA populations involving RNase R treatment followed by Polyadenylation and poly(A)+ RNA Depletion (RPAD), which removes linear RNA to near completion. High-throughput sequencing of RNA prepared using RPAD from human cervical carcinoma HeLa cells and mouse C2C12 myoblasts led to two surprising discoveries: (i) many exonic circRNA (EcircRNA) isoforms share an identical backsplice sequence but have different body sizes and sequences, and (ii) thousands of novel intronic circular RNAs (IcircRNAs) are expressed in cells. In sum, isolating high-purity circRNAs using the RPAD method can enable quantitative and qualitative analyses of circRNA types and sequence composition, paving the way for the elucidation of circRNA functions.
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Cites
Circular RNAs are a large class of animal RNAs with regulatory potency
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Natural RNA circles function as efficient microRNA sponges
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Landscape of transcription in human cells
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miRBase: annotating high confidence microRNAs using deep sequencing data
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Circular RNAs are abundant, conserved, and associated with ALU repeats
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Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed
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“Recent highthroughput RNA-Seq analyses have begun to identify the vast abundance of circRNAs (10,14), uncovering their tissue specificity and evolutionary conservation (10,11,14).”
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Circular intronic long noncoding RNAs
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Cited by
The Biogenesis, Functions, and Challenges of Circular RNAs
Li, X., Yang, L., & Chen, L.-L. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.034 · Cited by 2,062
Circular RNA in cardiovascular disease
Altesha, M., Ni, T., Khan, A., Liu, K., & Zheng, X. (2019) · Journal of Cellular Physiology · doi:10.1002/jcp.27384 · Cited by 517
Biogenesis and Regulatory Roles of Circular RNAs
Yang, L., Wilusz, J. E., & Chen, L.-L. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-125117 · Cited by 299
Circular RNAs in Muscle Function and Disease
Greco, S., Cardinali, B., Falcone, G., & Martelli, F. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19113454 · Cited by 89
Functions of Circular RNA in Human Diseases and Illnesses
Gu, A., Jaijyan, D. K., Yang, S., Zeng, M., Pei, S., & Zhu, H. (2023) · Non-Coding RNA · doi:10.3390/ncrna9040038 · Cited by 65
Metadata
- Authors
- Panda, A. C., De, S., Grammatikakis, I., Munk, R., Yang, X., Piao, Y., Dudekula, D. B., Abdelmohsen, K., & Gorospe, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-04-21
- Volume
- 45
- Issue
- 12
- Pages
- e116-e116
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2606437368
- Cited by
- 197
- References
- 9
- FWCI
- 7.67
- Type
- journal article
- Language
- en
- Open access
- gold
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- Panda, A. C., De, S., Grammatikakis, I., Munk, R., Yang, X., Piao, Y., Dudekula, D. B., Abdelmohsen, K., & Gorospe, M. (2017). High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx297
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