Identification and functional prediction of soybean CircRNAs involved in low-temperature responses

Wang, Xuesong; Chang, Xingchao; Ya, Jing; Zhao, Jialiang; Fang, Qingwei; Sun, Mingyang; Zhang, Yanzheng; Li, Wenbin; Li, Yongguang

doi:10.1016/j.jplph.2020.153188

Cited by 29 publications

(23 citation statements)

References 57 publications

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“…Fifty-five of these circRNAs possessed over one such binding site, resembling the prior finding on Brassica rapa (Liu et al ., 2022a). According to Wang et al (2020), best efficacy could be occasionally sustained by the mismatches in miRNA target sites rather than the ideally paired sites.…”

Section: Discussionmentioning

confidence: 99%

Identification and functional prediction of sugar beet circRNAs involved in drought responses

Zou

Guo

Zhao

et al. 2022

Preprint

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Drought is one of the most common abiotic constraints on the quality and productivity of crops on a global scale. Despite the rapidly updating information on circRNAs (circular RNAs), their roles in the anti-drought regulation of sugar beet are least understood. As a newly recognized class of non-coding RNAs, circRNAs exert crucial effects on miRNA (microRNA) functionality, as well as on transcriptional regulation. To clarify the mechanism of how circRNAs of sugar beet respond to drought stress, deep sequencing was employed to characterize these circRNAs in a genome-wide manner under drought treatment. Our results identify a total of 17 differentially expressed circRNAs. As revealed by the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology outcomes, circRNAs were found capable and involved in drought-responsive events. Utilizing the target genes exhibiting direct/indirect associations with drought resistance, we established a circRNA–miRNA–mRNA meshwork based on the circRNAs that were expressed differentially. The probable sponge functions of novel_circ_0000442 and novel_circ_0000443 were exerted by targeting ath-miR157d. This helped regulate the expression of relevant target genes, including BVRB_1 g004570, BVRB_1 g005450, and BVRB_1 g005790, that were involved in drought response. Apart from offering novel understandings of anti-drought mechanisms, our findings lay a basis for probing deeper into the intricate regulatory networks of sugar beet genes.

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Section: Discussionmentioning

confidence: 99%

Identification and functional prediction of sugar beet circRNAs involved in drought responses

Zou

Guo

Zhao

et al. 2022

Preprint

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“…Previous studies believed that circRNA was a byproduct of the transcription process (Cocquerelle et al 1993;Memczak et al 2013), but more and more studies in the past decade have confirmed that circRNA is a very important type of non-coding RNA, which plays a crucial role in a variety of biological processes (Chen et al 2017a). Most of the researches on the function of circRNA have focused on mammals (Salzman et al 2012), however, circRNA has also been identified in some plants, including Arabidopsis (Chen et al 2017a), rice (Lu et al 2015), wheat (Wang et al 2017), and soybean (Wang et al 2020). In present study, transcriptome sequencing and identification of the circRNA in the leaves of B. distachyon under dehydrated stress were performed.…”

Section: Discussionmentioning

confidence: 99%

“…The discovery of circRNA has been for decades, and it was once considered a by-product of splicing errors (Sanger et al 1976;Kos et al 1986). However, with the continuous development of high-throughput deep sequencing technology and bioinformatics tools, a variety of circRNAs have been discovered and identified in many organisms, such as humans (Jeck et al 2013), fruit flies (Westholm et al 2014), mice (Fan et al 2015), zebrafish (Shen et al 2017), Arabidopsis (Ye et al 2015), rice and soybeans (Wang et al 2020). These researches confirmed that circRNA is ubiquitous in eukaryotes.…”

Section: Introductionmentioning

confidence: 92%

“…Ye et al (2015Ye et al ( , 2016 identified 6,012 and 2,806 circRNAs from Arabidopsis leaves and rice seedling root tissues, respectively. In addition to these two well-known model plants, circRNA has also been identified in other monocot and dicot species, such as soybean (Wang et al 2020), barley (Behrooz et al 2016), and wheat (Xu et al 2019). Similar to the expression pattern of circRNA in animals (Westholm et al 2014;Fan et al 2015), circRNA in plants also exhibits tissue specificity and responds to environmental stress (Lu et al 2015;Behrooz et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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Identification of Drought-Responsive CircRNAs in Leaves of Brachypodium distachyon

Feng¹

2021

IJAB

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Brachypodium distachyonis currently recognized as a model organism in Gramineae, especially for temperate grains. Research on its dehydrationresponse mechanism is beneficial for elucidating the complex drought regulation network in temperate grains. The circRNA is an important type of non-coding RNA in organisms, which could involve in various biological processes. By sequencing the transcriptome of the leaves of B. distachyonunder desiccationtreatmentand normal condition, a total of 737 circRNAs were obtained in this study, of which 332 and 265 were up-regulated and 265 down-regulated, respectively, with 140 insignificant differences. There were 229 and 303 circRNAs specifically expressed under CK and drought,respectively and 204 were co-expressed. Bioinformatics methods were used to identify potential miRNA targets of differentially expressed circRNAs. Among them, 150 differentially expressed circRNAs had putative miRNA binding sites. According to the predicted miRNA with binding site, the target genes downstream of the miRNA were screened. In terms of the functional annotation of target genes, they are divided into seven categories: hormone-related, photosystem, stress response, regulation factor, ion transport, TF and ribosomal protein. These circRNAs involved in water deficitresponse may play a significant role in the drought response and defense of B. distachyon. This also provides new insights for the improvement of the dehydration regulation mechanism of B. distachyonand even temperate grains.© 2021 Friends Science Publishers

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“…However, increasing evidence showed that various circRNAs commonly existed in natural organisms with conservative sequences among different species. Until now, the identification of circRNAs and their possible roles have been explored in more than 20 species, including Archaea (8), plants (11,13,14), viruses (15)(16)(17)(18)(19), insects (20,21), and mammals (12,22,23). A small subset of circRNAs with different activities was confirmed to play vital roles in regulating individual growth and development, environmental stress, innate immunity, and disease occurrence (13,(24)(25)(26)(27)(28).…”

Section: Introductionmentioning

confidence: 99%

Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction

et al. 2022

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Circular RNAs (circRNAs) as novel regulatory molecules have been recognized in diverse species, including viruses. The virus-derived circRNAs play various roles in the host biological process and the life cycle of the viruses. This review summarized the circRNAs from the DNA and RNA viruses and discussed the biogenesis of viral and host circRNAs, the potential roles of viral circRNAs, and their future perspective. This review will elaborate on new insights gained on viruses encoded circRNAs during virus infection.

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Identification and functional prediction of soybean CircRNAs involved in low-temperature responses

Cited by 29 publications

References 57 publications

Identification and functional prediction of sugar beet circRNAs involved in drought responses

Identification and functional prediction of sugar beet circRNAs involved in drought responses

Identification of Drought-Responsive CircRNAs in Leaves of Brachypodium distachyon

Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction

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