The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Transcriptome-wide investigation of circular RNAs in rice
Open accessAbstract
Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs.
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Circular RNAs are a large class of animal RNAs with regulatory potency
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Circular RNAs are abundant, conserved, and associated with ALU repeats
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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
The biogenesis and emerging roles of circular RNAs
Chen, L.-L. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.32 · Cited by 1,743
Circular RNA Expression: Its Potential Regulation and Function
Salzman, J. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.03.002 · Cited by 804
Circular RNA and its mechanisms in disease: From the bench to the clinic
Han, B., Chao, J., & Yao, H. (2018) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2018.01.010 · Cited by 788
Self-citationPlant Noncoding RNAs: Hidden Players in Development and Stress Responses
Yu, Y., Zhang, Y., Chen, X., & Chen, Y. (2019) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100818-125218 · Cited by 396
Metadata
- Authors
- Lu, T., Cui, L., Zhou, Y., Zhu, C., Fan, D., Gong, H., Zhao, Q., Zhou, C., Zhao, Y., Lu, D., Luo, J., Wang, Y., Tian, Q., Feng, Q., Huang, T., & Han, B.
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2015-10-13
- Volume
- 21
- Issue
- 12
- Pages
- 2076-2087
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- OpenAlex
- W2177654732
- Cited by
- 416
- References
- 8
- FWCI
- 12.74
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Lu, T., Cui, L., Zhou, Y., Zhu, C., Fan, D., Gong, H., Zhao, Q., Zhou, C., Zhao, Y., Lu, D., Luo, J., Wang, Y., Tian, Q., Feng, Q., Huang, T., & Han, B. (2015). Transcriptome-wide investigation of circular RNAs in rice. RNA. https://doi.org/10.1261/rna.052282.115
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