Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

Liu, Ruiqi; Ma, Yue; Guo, Tao; Li, Guanglin

doi:10.1016/j.xplc.2022.100430

Cited by 26 publications

(16 citation statements)

References 176 publications

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“…In addition, the expression level of Vv-CircPTCD1 is remarkably decreased during salt stress after 5 days, while the host gene never occurred (Figure 2B, C). Those results imply that the Vv-CircPTCD1 plays a role during abiotic stress, in which the expression of circRNA potentially is controlled on the condition of specific abiotic stress, at least during the processing or degradation pathway [58].…”

Section: Discussionmentioning

confidence: 82%

Transgenic Phenotypic Differences of Grapevine Circular RNA Between Arabidopsis and Grapevine Callus Imply the Species-dependent Functions of Vv-circPTCD1

Ren¹,

Li²,

Liu³

et al. 2023

Preprint

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Circular RNAs (circRNAs) served as covalently closed single-stranded RNAs have been proposed to influence plant development and stress resistance. Grapevine is the most economically valuable fruit crops cultivated worldwide and threaten by various abiotic stresses. Herein, we reported that a circRNA (Vv-circPTCD1) processed from the second exon of a pentatricopeptide repeat family gene PTCD1 was preferentially expressed in leaves and responded to salt and drought but not heat stress in grapevine. Additionally, the second exon sequence of PTCD1 was highly conserved but the biogenesis of Vv-circPTCD1 is species-dependent in plants. It was further found that the overexpressed Vv-circPTCD1 can slightly decreased abundance of the cognate host gene and the neighboring genes were barely affected in grapevine callus. Furthermore, we also successfully overexpressed the Vv-circPTCD1, and found that the Vv-circPTCD1 deteriorated the growth during heat, salt, and drought stresses in Arabidopsis. However, the biological effects on grapevine callus were not always consistent with that of Arabidopsis. Interestingly, we found that the transgenic plants of linear counterpart sequence also conferred the same phenotypes as that of circRNA during the three stress conditions, no matter what species. Those results imply that although the sequences are conserved, the biogenesis and functions of Vv-circPTCD1 are species-dependent. Our results indicate that the plant circRNA function investigation should be conducted in homologous species, which support valuable reference for further plant circRNA studies.

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Section: Discussionmentioning

confidence: 82%

Transgenic Phenotypic Differences of Grapevine Circular RNA Between Arabidopsis and Grapevine Callus Imply the Species-dependent Functions of Vv-circPTCD1

Ren¹,

Li²,

Liu³

et al. 2023

Preprint

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“…Many circRNAs were discovered and identified in human [ 11 ], rat [ 13 ], and zebrafish [ 12 ], and were shown to have important roles in various biological and developmental processes. In contrast to the comprehensive study of circRNAs in animals, circRNAs research in plants is still in its infancy [ 31 ]. It was not until the first discovery of circRNAs in Arabidopsis thaliana in 2014 [ 15 ] that research on circRNA in plants began.…”

Section: Discussionmentioning

confidence: 99%

Identification and Characterization of Circular RNAs Involved in the Flower Development and Senescence of Rhododendron delavayi Franch

Xiao

Zhang

et al. 2022

IJMS

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Floral development and senescence are a crucial determinant for economic and ornamental value. CircRNAs play an essential role in regulating plant growth and development; however, there is no systematic identification of circRNAs during the lifespan of flowers. This study aims to explore the expression profile and functional role of circRNAs in the full flowering stages of Rhododendron delavayi Franch. We carried out transcriptome sequencing of the six stages of Rhododendron delavayi Franch flowers to identify the circular RNA expression profile. In addition, using bioinformatics methods, we explored the functions of circRNAs, including analysis of the circRNA-miRNA-mRNA network, short time-series expression miner (STEM), and so on. We identified 146 circRNAs, of which 79 were differentially expressed from the budding to fading stages. Furthermore, using STEM analysis, one of the 42 circRNA expression model profiles was significantly upregulated during the senescence stage, including 16 circRNAs. Additionally, 7 circRNA-miRNA-mRNA networks were constructed with 10 differentially expressed circRNAs, in which some target mRNA may regulate the development and senescence of the Rhododendron flowers. Finally, by analyzing the correlation between circRNAs and mRNA, combined with existing reports, we proposed that circRNAs play a regulatory role during flower development and senescence by mediating the jasmonate signaling pathway. Overall, these results provide new clues to the potential mechanism of circRNAs acting as novel post-transcriptional regulators in the development and senescence process of flowers.

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“…Some circRNAs have been shown to be translated into short peptides in animal systems through internal ribosome entry sites (IRES) and N6-methyladenosine (m6A) modifications. These IRES and m6A features have been identified in plant circR-NAs, but the translation of plant circRNAs has not yet been shown (R. Liu et al, 2022;Y. Wang et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…There are relatively few studies that have concretely demonstrated functions of specific plant circRNAs in overexpression or knockdown experiments (V. M. Conn et al, 2017;Z. Gao et al, 2019;R. Liu et al, 2022;Xia et al, 2023;Zhou et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

Budnick,

Franklin,

Utley

et al. 2024

The Plant Genome

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Circular RNAs (circRNAs) are covalently closed single‐stranded RNAs, generated through a back‐splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high‐confidence circRNA‐expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.

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Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

Cited by 26 publications

References 176 publications

Transgenic Phenotypic Differences of Grapevine Circular RNA Between Arabidopsis and Grapevine Callus Imply the Species-dependent Functions of Vv-circPTCD1

Transgenic Phenotypic Differences of Grapevine Circular RNA Between Arabidopsis and Grapevine Callus Imply the Species-dependent Functions of Vv-circPTCD1

Identification and Characterization of Circular RNAs Involved in the Flower Development and Senescence of Rhododendron delavayi Franch

Long‐ and short‐read sequencing methods discover distinct circular RNA pools in Lotus japonicus

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