Integrative analysis of <i>Arabidopsis thaliana</i> transcriptomics reveals intuitive splicing mechanism for circular RNA

Sun, Xiaoyong; Wang, Lin; Ding, Jiechao; Wang, Yanru; Wang, Jiansheng; Zhang, Xiaoyang; Che, Yulei; Liu, Ziwei; Zhang, Xinran; Ye, Jiazhen; Wang, Jie; Sablok, Gaurav; Deng, Zhiping; Zhao, Hongwei

doi:10.1002/1873-3468.12440

Cited by 86 publications

(67 citation statements)

References 23 publications

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“…Recently, with the development of high‐throughput sequencing and bioinformatics, a huge number of circRNAs have been identified in Archaea, Caenorhabditis elegans , mice, and humans (Danan et al ; Salzman et al , 2012b, Memczak et al , Zhang et al ). Although circRNAs in plants have been identified (Wang et al , Lu et al , Sun et al ), the studies were relatively limited and the molecular functions of circRNAs need further study. In tomato, circRNAs have only been identified in ‘Rui Xin’ fruit under chilling injury (Zuo et al ).…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Wang

Gao

et al. 2017

Physiologia Plantarum

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Circular RNAs (circRNAs) are a large class of non-coding endogenous RNAs that could act as competing endogenous RNAs (ceRNAs) to terminate the mRNA targets' suppression of miRNAs. To elucidate the intricate regulatory roles of circRNAs in the ethylene pathway in tomato fruit, deep sequencing and bioinformatics methods were performed. After strict screening, a total of 318 circRNAs were identified. Among these circRNAs, 282 were significantly differentially expressed among wild-type and sense-/antisense-LeERF1 transgenic tomato fruits. Besides, 1254 target genes were identified and a large amount of them were found to be involved in ethylene pathway. In addition, a sophisticated regulatory model consisting of circRNAs, target genes and ethylene was set up. Importantly, 61 circRNAs were found to be potential ceRNAs to combine with miRNAs and some of the miRNAs had been revealed to participate in the ethylene signaling pathway. This research further raised the possibility that the ethylene pathway in tomato fruit may be under the regulation of various circRNAs and provided a new perspective of the roles of circRNAs.

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Section: Discussionmentioning

confidence: 99%

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Wang

Gao

et al. 2017

Physiologia Plantarum

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“…Evolutionary conservation of circRNAs circRNAs are present in most organisms, including Archaea, plants, yeast, and most metazoans (Danan et al, 2012;Wang et al, 2014;Broadbent et al, 2015;Lu et al, 2015;Sun et al, 2016;Ji et al, 2019). However, it is not clear how they have evolved, as they seem to be produced by different mechanisms.…”

Section: Circrna Properties and Featuresmentioning

confidence: 99%

Past, present, and future of circ RNA s

2019

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Exonic circular RNAs (circRNAs) are covalently closed RNA molecules generated by a process named back‐splicing. circRNAs are highly abundant in eukaryotes, and many of them are evolutionary conserved. In metazoans, circular RNAs are expressed in a tissue‐specific manner, are highly stable, and accumulate with age in neural tissues. circRNA biogenesis can regulate the production of the linear RNA counterpart in cis as back‐splicing competes with linear splicing. Recent reports also demonstrate functions for some circRNAs in trans: Certain circRNAs interact with microRNAs, some are translated, and circRNAs have been shown to regulate immune responses and behavior. Here, we review current knowledge about animal circRNAs and summarize new insights into potential circRNA functions, concepts of their origin, and possible future directions in the field.

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“…These complementary sequences were short, ranging in size from 4 to 5 nucleotides (Table ). Similarly, in Arabidopsis thaliana samples, only 37% of the circRNA had some complementary sequences near the splice sites . These observations indicate that in addition to complementary sequences, there must exist other elements that guarantee circularization.…”

Section: Discussionmentioning

confidence: 95%

“…With the advent of high‐throughput sequencing of nonpolyadenylated RNA transcripts, many studies have revealed large numbers of circRNA that are endogenous to eukaryotes (e.g. humans, mice, zebrafish, worms, fruit flies, plants), many of which are abundant and stable . CircRNA have no free 3′ or 5′ end, so these RNA cannot be detected by molecular techniques that rely on polyadenylated free RNA ends.…”

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confidence: 99%

Newly identified APN splice isoforms suggest novel splicing mechanisms may underlie circRNA circularization in moth

et al. 2019

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Circular RNA (circ RNA ) have long been considered by‐products of splicing errors, but the coordination of RNA transcription and exon circularization events remains poorly understood. Here, we investigated this question using genes encoding aminopeptidases N ( APN s), which are receptors of Bacillus thuringiensis toxins, in the cotton bollworm, Helicoverpa armigera . We cloned and sequenced the cDNA of ten APN genes ( Ha APN 1‐10 ) located in the same APN gene cluster, and detected 20 and 14 novel splicing isoforms with exon skipping in Ha APN 1 and Ha APN 3 , respectively, whereas no or very few variants were found in the remaining genes. Further study identified 14 and 6 circular RNA (circ RNA ) in Ha APN 1 and Ha APN 3, respectively. Neither novel splicing isoforms nor circ RNA were detected in Ha APN 2 and Ha APN 5 . Distinct from the conventional GT / AG splicing signal, short co‐directional repeats were involved in the splicing of the linear and circular isoforms of Ha APN 1 and Ha APN 3 . Identification of the splice sites revealed that the linear isoforms may be related in some way to the circularization. Moreover, phylogenetic analysis and detection of circ RNA of the APN gene of the diamondback moth, Plutella xylostella ( Px APN 3 ), showed that circ RNA formation is relatively conserved during the lepidopteran evolutionary process. These results contribute to an improved understanding of lepidopteran APN s and this novel class of insect circ RNA .

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Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA

Cited by 86 publications

References 23 publications

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato

Past, present, and future of circ RNA s

Newly identified APN splice isoforms suggest novel splicing mechanisms may underlie circRNA circularization in moth

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