Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Ye, Chu-Yu; Zhang, Xingchen; Chu, Qinjie; Liu, Chen; Yu, Yifan; Jiang, Weiqin; Zhu, Qian; Fan, Longjiang; Guo, Longbiao

doi:10.1080/15476286.2016.1245268

Cited by 115 publications

(85 citation statements)

References 40 publications

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“…circRNAs are widespread and diverse in both animals and plants and have potential regulatory functions . In plants, circRNAs are closely associated with development and stress-induced responses Ye et al, 2015Ye et al, , 2017. Here, we demonstrated that circRNAs are involved in the rice-M. oryzae interaction.…”

Section: Discussionmentioning

confidence: 76%

“…Since alternative back splicing is required for the biogenesis and diversification of circRNAs in rice Ye et al, 2017), we hypothesized more diverse circRNAs in IR25 may be attributed to more complicated alternative splicing in IR25 than in LTH. Therefore, we annotated the downstream 59 back-splice sites and upstream 39 back-splice sites from all the identified circRNAs.…”

Section: Alternative Splicing Contributes To the Increased Circrna DImentioning

confidence: 99%

“…circRNAs regulate gene expression in animals through different mechanisms, such as miRNA sponges, specific RNA-RNA interactions, and affecting alternative splicing . Since the identification of their roles in regulating gene expression in animals (Memczak et al, 2013), circRNAs have also been identified in different plant species, including Arabidopsis (Arabidopsis thaliana), rice, wheat (Triticum aestivum), barley (Hordeum vulgare), maize (Zea mays), tomato (Solanum lycopersicum), potato (Solanum tuberosum), soybean (Glycine max), cotton (Gossypium hirsutum), and kiwifruit (Actinidia deliciosa; Wang et al, 2014Wang et al, , 2017bWang et al, , 2017cLu et al, 2015;Ye et al, 2015Ye et al, , 2017Darbani et al, 2016;Zuo et al, 2016;Chen et al, 2017Chen et al, , 2018Zhao et al, 2017).…”

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confidence: 99%

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circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

Fan

Quan²,

et al. 2019

Plant Physiol.

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ORCID IDs: 0000-0002-6747-4302 (J.F.); 0000-0003-4066-4875 (W.-M.W.).Circular RNAs (circRNAs) play roles in various biological processes, but their functions in the rice (Oryza sativa) response to Magnaporthe oryzae remain elusive. Here, we demonstrate that circRNAs are involved in the rice-M. oryzae interaction using comparative circRNA-sequencing and transgenic approaches. We identified 2932 high-confidence circRNAs from young leaves of the blast-resistant accession International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake (IR25) and the blast-susceptible accession Lijiangxin Tuan Heigu (LTH) under M. oryzae-infected or uninfected conditions; 636 were detected specifically upon M. oryzae infection. The circRNAs in IR25 were significantly more diverse than those in LTH, especially under M. oryzae infection. Particularly, the number of circRNAs generated per parent gene was much higher in IR25 than in LTH and increased in IR25 but decreased in LTH upon M. oryzae infection. The higher diversity of circRNAs in IR25 was further associated with more frequent 39 and 59 alternative back-splicing and usage of complex splice sites. Moreover, a subset of circRNAs was differentially responsive to M. oryzae in IR25 and LTH. We further confirmed that circR5g05160 promotes rice immunity against M. oryzae. Therefore, our data indicate that circRNA diversity is associated with different responses to M. oryzae infection in rice and provide a starting point to investigate a new layer of regulation in the rice-M. oryzae interaction.

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Section: Discussionmentioning

confidence: 76%

Section: Alternative Splicing Contributes To the Increased Circrna DImentioning

confidence: 99%

mentioning

confidence: 99%

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circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

Fan

Quan²,

et al. 2019

Plant Physiol.

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“…Increasing data have shown that a variety of organisms could generate circRNAs by back-splicing, including Drosophila [25], rice [26], silkworm [27], zebrafish [28], and humans [29]. In addition to cellular transcripts, viral transcripts were found to form circRNAs in KSHV-infected primary effusion lymphoma cells, EBV-infected cells [20,21] or HPV16 [23].…”

Section: Discussionmentioning

confidence: 99%

HBV pgRNA can generate a circRNA with two junction sites

Zhu

Liang

Pan

et al. 2020

Preprint

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To verify whether Hepatitis B virus (HBV) can form circRNA, the circRNA sequencing results of the HBV-positive HepG 2.2.15 hepatocarcinoma cell line were compared with the HBV genome. A novel circRNA, named as HBV_circ_1, was mapped to the 489-2985 nt region of the HBV genome (GenBank accession No. KU668446.1), which was derived from HBV pgRNA and has two junction sites. A partial fragment of the pgRNA (corresponding to HBV DNA genome 489-3,182-2,985nt) was resected and then connected to form a junction site of HBV_circ_1 (corresponding to HBV DNA genome 489/2985nt). The 5′-terminal region (corresponding to HBV DNA genome 1,820-1,932nt) of pgRNA was repeated with the region of pgRNA at the 3′-terminal region. Another junction site of HBV_circ_1 (corresponding to HBV DNA genome 1820nt) was formed in a manner similar to DNA homologous recombination mediated by repeats of pgRNA. Moreover, this RNA homologous recombination mediated by the repeats of pgRNA does not have tissue specificity and genus specificity. Reverse transcription PCR, northern blotting, and tissue in situ hybridization confirmed the existence of HBV_circ_1 in HepG2.2.15 cells and HBV related hepatocellular carcinoma (HCC) tissue. This study expands our understanding of circRNA generation mechanisms, and provide a new perspective for understanding the molecular pathogenesis of the virus.

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“…Indeed, some methods such as circseq_cup [23] and the oven-fresh CIRC-full method[24] can generate full-length sequence for circRNA however only after the BSJ determination, which the accuracy and integrity of the circRNA sequences are largely not validated yet. Since there is still lack of a benchmark or gold standard to evaluate circRNA detection fairly, only a small portion of circRNAs predicted by the reference-based methods can be experimentally validated [23]. Moreover, accurate detection and quantification of circRNA isoforms for a definite BSJ is far beyond the scope of current methods.…”

Section: Introductionmentioning

confidence: 99%

Reference-free andde novoIdentification of Circular RNAs

Qin

Lin

et al. 2020

Preprint

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Background: Early studies have unveiled multiple regulatory functions of circular RNAs (circRNAs); however, accurate detection and quantification of circRNAs, especially in understudied organisms, is unsolved yet. Results:In this study, we developed a new reference-free method, namely Cirit, to de novo detect circRNAs with sequence support from the next generation sequencing (NGS) transcriptome. The Cirit showed remarkable performance in accurate detection and quantification of circRNAs via comparing with current methods from different aspects. Using Cirit, we detected 28,813 nonredundant human circRNAs from 91 transcriptome datasets, as well as 2,385 circRNAs from four understudied organisms.Subsequent analyses found that the majority of human circRNAs expressed spatiotemporally; only a very small portion of circRNAs were back-splice junction (BSJ)-consistent (maximally 5.17%) or sequence-consistent (under 2%). Furthermore, circRNA genesis were relatively flexible that only about 60% of human circRNAs used the canonical GT-AG pattern for back-splice. The inconsistent expression of circRNAs challenges their roles as precise transcriptional regulators. Conclusions:In summary, the reference-free method provides a straightforward and universal way for reliable circRNA research. It will largely boost the successful rate in designing highly specific probes to monitor circRNA behavior in cell. In particular, it brings circRNA research to the organisms that have no genome or draft genome.

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Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Cited by 115 publications

References 40 publications

circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

circRNAs Are Involved in the Rice-Magnaporthe oryzae Interaction

HBV pgRNA can generate a circRNA with two junction sites

Reference-free andde novoIdentification of Circular RNAs

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