| [1] |
Patop IL, Wüst S, Kadener S. 2019. Past, present, and future of circRNAs. The EMBO Journal 38:e100836 doi: 10.15252/embj.2018100836 |
| [2] |
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. 2012. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 7:e30733 doi: 10.1371/journal.pone.0030733 |
| [3] |
Kristensen LS, Andersen MS, Stagsted LVW, Ebbesen KK, Hansen TB, et al. 2019. The biogenesis, biology and characterization of circular RNAs. Nature Reviews Genetics 20:675−91 doi: 10.1038/s41576-019-0158-7 |
| [4] |
Liu CX, Chen LL. 2022. Circular RNAs: Characterization, cellular roles, and applications. Cell 185:2390 doi: 10.1016/j.cell.2022.06.001 |
| [5] |
Chen LL, Bindereif A, Bozzoni I, Chang HY, Matera AG, et al. 2023. A guide to naming eukaryotic circular RNAs. Nature Cell Biology 25:1−5 doi: 10.1038/s41556-022-01066-9 |
| [6] |
Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, et al. 2013. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19:141−57 doi: 10.1261/rna.035667.112 |
| [7] |
Zhang C, Kang Y, Kong F, Yang Q, Chang D. 2022. Hotspots and development frontiers of circRNA based on bibliometric analysis. Non-coding RNA Research 7:77−88 doi: 10.1016/j.ncrna.2022.03.001 |
| [8] |
Xu C, Zhang J. 2021. Mammalian circular RNAs result largely from splicing errors. Cell Reports 36:109439 doi: 10.1016/j.celrep.2021.109439 |
| [9] |
Robic A, Cerutti C, Demars J, Kühn C. 2022. From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1865:194815 doi: 10.1016/j.bbagrm.2022.194815 |
| [10] |
Jin L, Tang Q, Hu S, Chen Z, Zhou X, et al. 2021. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nature Communications 12:3715 doi: 10.1038/s41467-021-23560-8 |
| [11] |
Ragan C, Goodall GJ, Shirokikh NE, Preiss T. 2019. Insights into the biogenesis and potential functions of exonic circular RNA. Scientific Reports 9:2048 doi: 10.1038/s41598-018-37037-0 |
| [12] |
Robic A, Faraut T, Djebali S, Weikard R, Feve K, et al. 2019. Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs. RNA Biology 16:1190−204 doi: 10.1080/15476286.2019.1621621 |
| [13] |
Robic A, Hadlich F, Costa Monteiro Moreira G, Louise Clark E, Plastow G, et al. 2024. Innovative construction of the first reliable catalogue of bovine circular RNAs. RNA Biology 21:52−74 doi: 10.1080/15476286.2024.2375090 |
| [14] |
Yang L, Wilusz JE, Chen LL. 2022. Biogenesis and Regulatory Roles of Circular RNAs. Annual Review of Cell and Developmental Biology 38:263−89 doi: 10.1146/annurev-cellbio-120420-125117 |
| [15] |
Digby B, Finn S, Ó Broin P. 2024. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 25:527 doi: 10.1186/s12864-024-10420-0 |
| [16] |
Rebolledo C, Silva JP, Saavedra N, Maracaja-Coutinho V. 2023. Computational approaches for circRNAs prediction and in silico characterization. Briefings in Bioinformatics 24:bbad154 doi: 10.1093/bib/bbad154 |
| [17] |
Srinivasan A, Mroczko-Młotek E, Wojciechowska M. 2025. Circular RNA formation and degradation are not directed by universal pathways. International Journal of Molecular Sciences 26:726 doi: 10.3390/ijms26020726 |
| [18] |
Robic A, Kühn C. 2020. Beyond back splicing, a still poorly explored world: non-canonical circular RNAs. Genes 11:1111 doi: 10.3390/genes11091111 |
| [19] |
Ares M, Jr., Igel H, Katzman S, Donohue JP. 2024. Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition. Genes & Development 38:322−35 doi: 10.1101/gad.351764.124 |
| [20] |
Nielsen AF, Bindereif A, Bozzoni I, Hanan M, Hansen TB, et al. 2022. Best practice standards for circular RNA research. Nature Methods 19:1208−20 doi: 10.1038/s41592-022-01487-2 |
| [21] |
Drula R, Braicu C, Berindan-Neagoe I. 2024. Current advances in circular RNA detection and investigation methods: Are we running in circles? WIREs RNA 15:e1850 doi: 10.1002/wrna.1850 |
| [22] |
Ashwal-Fluss R, Meyer M, Pamudurti NR, Ivanov A, Bartok O, et al. 2014. circRNA biogenesis competes with pre-mRNA splicing. Molecular Cell 56:55−66 doi: 10.1016/j.molcel.2014.08.019 |
| [23] |
Starke S, Jost I, Rossbach O, Schneider T, Schreiner S, et al. 2015. Exon circularization requires canonical splice signals. Cell Reports 10:103−11 doi: 10.1016/j.celrep.2014.12.002 |
| [24] |
Ma XK, Xue W, Chen LL, Yang L. 2021. CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets. Methods 196:3−10 doi: 10.1016/j.ymeth.2021.02.008 |
| [25] |
Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, et al. 2016. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Research 26:1277−87 doi: 10.1101/gr.202895.115 |
| [26] |
Gao Y, Zhang J, Zhao F. 2018. Circular RNA identification based on multiple seed matching. Briefings in Bioinformatics 19:803−10 doi: 10.1093/bib/bbx014 |
| [27] |
Chen L, Wang C, Sun H, Wang J, Liang Y, et al. 2021. The bioinformatics toolbox for circRNA discovery and analysis. Briefings in Bioinformatics 22:1706−28 doi: 10.1093/bib/bbaa001 |
| [28] |
Robic A, Cerutti C, Kühn C, Faraut T. 2021. Comparative analysis of the circular transcriptome in muscle, liver and testis in three livestock species. Frontiers in Genetics 12:665153 doi: 10.3389/fgene.2021.665153 |
| [29] |
Gao Y, Wang J, Zhao F. 2015. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification. Genome Biology 16:4 doi: 10.1186/s13059-014-0571-3 |
| [30] |
Teng J, Gao Y, Yin H, Bai Z, Liu S, et al. 2024. A compendium of genetic regulatory effects across pig tissues. Nature Genetics 56:112−23 doi: 10.1038/s41588-023-01585-7 |
| [31] |
Liu S, Gao Y, Canela-Xandri O, Wang S, Yu Y, et al. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics 54:1438−47 doi: 10.1038/s41588-022-01153-5 |
| [32] |
Gruhl F, Janich P, Kaessmann H, Gatfield D. 2021. Circular RNA repertoires are associated with evolutionarily young transposable elements. eLife 10:e67991 doi: 10.7554/eLife.67991 |
| [33] |
Hansen TB, Venø MT, Damgaard CK, Kjems J. 2016. Comparison of circular RNA prediction tools. Nucleic Acids Research 44:e58 doi: 10.1093/nar/gkv1458 |
| [34] |
Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, et al. 2023. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nature Methods 20:1159−69 doi: 10.1038/s41592-023-01944-6 |
| [35] |
Hansen TB. 2018. Improved circRNA identification by combining prediction algorithms. Frontiers in Cell and Developmental Biology 6:20 doi: 10.3389/fcell.2018.00020 |
| [36] |
Zeng X, Lin W, Guo M, Zou Q. 2017. A comprehensive overview and evaluation of circular RNA detection tools. Computational Biology 13:e1005420 doi: 10.1371/journal.pcbi.1005420 |
| [37] |
Zeng X, Lin W, Guo M, Zou Q. 2019. Details in the evaluation of circular RNA detection tools: Reply to Chen and Chuang. PLoS Computational Biology 15:e1006916 doi: 10.1371/journal.pcbi.1006916 |
| [38] |
Chen CY, Chuang TJ. 2019. Comment on "A comprehensive overview and evaluation of circular RNA detection tools". PLoS Computational Biology 15:e1006158 doi: 10.1371/journal.pcbi.1006158 |
| [39] |
Chuang TJ, Chiang TW, Chen CY. 2023. Assessing the impacts of various factors on circular RNA reliability. Life Science 6:e202201793 doi: 10.26508/lsa.202201793 |
| [40] |
Zhang J, Chen S, Yang J, Zhao F. 2020. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications 11:90 doi: 10.1038/s41467-019-13840-9 |
| [41] |
Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. 2022. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. Briefings in Bioinformatics 23:bbab418 doi: 10.1093/bib/bbab418 |
| [42] |
Ayyildiz D, Bergonzoni G, Monziani A, Tripathi T, Döring J, et al. 2023. CAG repeat expansion in the Huntington's disease gene shapes linear and circular RNAs biogenesis. PLoS Genetics 19:e1010988 doi: 10.1371/journal.pgen.1010988 |
| [43] |
Chang S, Wang Y, Wang X, Liu H, Zhang T, et al. 2024. HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes. RNA Biology 21:834−48 doi: 10.1080/15476286.2024.2386500 |
| [44] |
Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, et al. 2019. CIRCexplorer3: a CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics 17:511−21 doi: 10.1016/j.gpb.2019.11.004 |