The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Increased complexity of circRNA expression during species evolution
Open accessAbstract
Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves. Quantification of RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns by Complementary Sequence Index (CSI) identifies that among all types of complementary sequences, SINEs, especially Alu elements in human, contribute the most for circRNA formation and that their diverse distribution across species leads to the increased complexity of circRNA expression during species evolution. Together, our integrated and comparative reference catalog of circRNAs in different species reveals a species-specific pattern of circRNA expression and suggests a previously under-appreciated impact of fast-evolved SINEs on the regulation of (circRNA) gene expression.
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Cites
pROC: an open-source package for R and S+ to analyze and compare ROC curves
Robin, X., Turck, N., Hainard, A., Tiberti, N., Lisacek, F., Sanchez, J.-C., & Müller, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-77 · Cited by 13,697
Circular RNAs are a large class of animal RNAs with regulatory potency
Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., et al. (2013) · Nature · doi:10.1038/nature11928 · Cited by 7,990
Circular RNAs are abundant, conserved, and associated with ALU repeats
Jeck, W. R., Sorrentino, J. A., Wang, K., Slevin, M. K., Burd, C. E., Liu, J., Marzluff, W. F., & Sharpless, N. E. (2013) · RNA · doi:10.1261/rna.035667.112 · Cited by 4,388
Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed
Rybak-Wolf, A., Stottmeister, C., Glažar, P., Jens, M., Pino, N., Giusti, S., Hanan, M., Behm, M., Bartok, O., Ashwal-Fluss, R., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.03.027 · Cited by 2,423 · cited 3×
“Expression profiling showed diverse expression patterns of circRNAs among cell types/tissues(13-17) with a significant enrichment of circRNAs in neurons/brains.(8,18-20) Interestingly, a single gene locus can produce multiple circRNAs, referred to as alternative circularization.”
BackgroundComplementary Sequence-Mediated Exon Circularization
Zhang, X.-O., Wang, H.-B., Zhang, Y., Lu, X., Chen, L.-L., & Yang, L. (2014) · Cell · doi:10.1016/j.cell.2014.09.001 · Cited by 1,999 · cited 3×
“Although inefficiently catalyzed by the spliceosome and generally expressed at low levels,(6-8) circRNA formation can be facilitated by both RNA pairing of orientation-opposite complementary sequences across flanking introns and protein factors that are capable of binding flanking introns to bridge unfavorable backspl…”
BackgroundMethodSelf-citationRegulation of circRNA biogenesis
Chen, L.-L., & Yang, L. (2015) · RNA Biology · doi:10.1080/15476286.2015.1020271 · Cited by 1,953
Self-citationThe 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
Self-citationThe Evolutionary Landscape of Alternative Splicing in Vertebrate Species
Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science · doi:10.1126/science.1230612 · Cited by 1,063
Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
Merkin, J., Russell, C., Chen, P., & Burge, C. B. (2012) · Science · doi:10.1126/science.1228186 · Cited by 972
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
Self-citationCircbank: a comprehensive database for circRNA with standard nomenclature
Liu, M., Wang, Q., Shen, J., Yang, B. B., & Ding, X. (2019) · RNA Biology · doi:10.1080/15476286.2019.1600395 · Cited by 554
Specific expression and functions of circular RNAs
Misir, S., Wu, N., & Yang, B. B. (2022) · Cell Death & Differentiation · doi:10.1038/s41418-022-00948-7 · Cited by 469
Circular RNAs open a new chapter in cardiovascular biology
Aufiero, S., Reckman, Y. J., Pinto, Y. M., & Creemers, E. E. (2019) · Nature Reviews Cardiology · doi:10.1038/s41569-019-0185-2 · Cited by 357
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
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Metadata
- Authors
- Dong, R., Ma, X.-K., Chen, L.-L., & Yang, L.
- Venue
- RNA Biology
- Publisher
- Informa UK Limited
- Published
- 2017-01-19
- Volume
- 14
- Issue
- 8
- Pages
- 1064-1074
- ISSN
- 1547-6286 (ISSN-L)
- 1555-8584
- OpenAlex
- W2565364968
- Cited by
- 219
- References
- 9
- FWCI
- 7.37
- Type
- journal article
- Language
- en
- Open access
- bronze
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