Systematic investigation of circular RNAs in Ascosphaera apis, a fungal pathogen of honeybee larvae

Guo, Rui; Chen, Dafu; Chen, Huazhi; Fu, Zhanli; Xiong, Chuan; Hou, Chunsheng; Zheng, Yusheng; Guo, Yang; Wang, Haipeng; Du, Yuguang; Diao, Qingyun

doi:10.1016/j.gene.2018.07.076

Cited by 24 publications

(20 citation statements)

References 43 publications

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“…1 4 Recent evidence suggests that circRNAs are able to play very important roles in alternative splicing, transcriptional regulation, and the regulation of source gene expression. With the rapid development of high-throughput sequencing technologies and bioinformatics analyses, circRNAs have been identified in many species, including humans [1,8,9], mice [10], cattle [11], grass carp [12], zebrafish [13], chickens [14], pigs [15], rice [16], barley [17], Arabidopsis thaliana [18], Archaea [19], Caenorhabditis elegans [20], A. apis [21], Nosema ceranae [22], and…”

Section: Validation Of Decircrnas In the A C Cerana Worker's Midgutmentioning

confidence: 99%

“…To verify the back-splicing junction of circRNA, five circRNAs were randomly selected for PCR verification. Special divergent and convergent primers for each candidate circRNA were designed using DNAMAN (Lynnon Biosoft) software following previously described method [21] (Additional file 2: Table S1). Total RNA of Ac1 and Ac2 were isolated with AxyPre RNA extraction Kit (Axygen) and divided into three portions, one of which was treated with 3 U/mg RNase R (Geneseed) for 15 min at 37 °C to remove linear RNA followed by reverse transcription with hexamer to synthesize the first strand cDNA, another one portion of RNA was reversed transcribed with OligdT primer to synthesize the first strand cDNA, and the third one The PCR products were examined on 2% agarose gel electrophoresis with Genecolor (Gene-Bio) staining.…”

Section: Pcr Confirmation Of Novel Circrna With Convergent and Divergmentioning

confidence: 99%

“…To verify the reliability of RNA-seq data, we randomly selected 10 circRNAs for Real time quantitative PCR (RT-qPCR). special divergent primers were designed and cDNA was synthesized according to the method [21] above (Additional file 11: Table S10).…”

Section: Real Time Quantitative Pcr Validation Of Decircrnamentioning

confidence: 99%

“…a number of circRNAs have been identified in humans [1,8,9], animals [10][11][12][13][14][15], plants [16][17][18], and microorganisms [19][20][21][22][23]. For example, Salzman et al [9] predicted 46866 circRNAs in 15 human cell types and found that these circRNAs have potential regulatory functions.…”

mentioning

confidence: 99%

“…Lu's research group predicted 2354 circRNAs from rice using next-generation sequencing and further revealed that these circRNAs had a considerable number of isoforms [16]. Guo et al [21] conducted high-throughput sequencing of mycelia and spore samples of Ascosphaera apis and discovered 551 circRNAs with a length of 200-600 nt using bioinformatics analysis; additionally, the authors investigated the regulatory networks between circRNAs and miRNAs and found complex interactions among them. Thus far, there is little research on insect circRNA, and the knowledge of circRNAs in insects, including honeybees, is still lacking [24][25][26].…”

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confidence: 99%

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Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut ofApis cerana ceranaworkers

Chen

et al. 2019

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Background: Circular RNAs (circRNAs) are newly discovered noncoding RNAs (ncRNAs) that play key roles in various biological functions, such as the regulation of gene expression and alternative splicing. CircRNAs have been identified in some species, including western honeybees. However, the understanding of honeybee circRNA is still very limited, and to date, no study on eastern honeybee circRNA has been conducted. Here, the circRNAs in the midguts of Apis cerana cerana workers were identified and validated, and the regulatory networks were constructed.Differentially expressed circRNAs (DEcircRNAs) and the corresponding competitively endogenous RNA (ceRNA) networks in the development of the worker's midgut were further investigated.Results: Here, 7-and 10-day-old A. c. cerana workers' midguts (Ac1 and Ac2) were sequenced using RNA-seq, and a total of 9589 circRNAs were predicted using bioinformatics. These circRNAs were approximately 201-800 nt in length and could be classified into six types; the annotated exonic circRNAs were the most abundant.Additionally, five novel A. c. cerana circRNAs were confirmed by PCR amplification and Sanger sequencing, indicating the authenticity of A. c. cerana circRNAs.Interestingly, novel_circ_003723, novel_circ_002714, novel_circ_002451 and novel_circ_001980 were the most highly expressed circRNAs in both Ac1 and Ac2, which is indicative of their key roles in the development of the midgut. Moreover, 55DEcircRNAs were identified in the Ac1 vs Ac2 comparison group, including 34 upregulated and 21 downregulated circRNAs. Further investigation showed that the 3 source genes of circRNAs were classified into 34 GO terms and were involved in 141 KEGG pathways. In addition, the source genes of DEcircRNAs were categorized into 10 GO terms and 15 KEGG pathways, which demonstrated that the corresponding DEcircRNAs may affect the growth, development, and material and energy metabolisms of the worker's midgut by regulating the expression of the related source genes. Additionally, the circRNA-miRNA regulatory networks were constructed and analyzed, and the results demonstrated that 1060 circRNAs can bind to 74 miRNAs and that 71.51% of circRNAs can be linked to only one miRNA. Furthermore, the DEcircRNA-miRNA-mRNA networks were constructed and explored, and the results indicate that the 13 downregulated circRNAs can bind to eight miRNAs and to 29 target genes. In addition, the results indicate that the 16 upregulated circRNAs can bind to 9 miRNAs and to 29 target genes, demonstrating that DEcircRNAs are likely involved in the regulation of midgut development via ceRNA mechanisms. Moreover, the regulatory networks of miR-6001-y-targeted DEcircRNAs were analyzed, and the results showed that eight DEcircRNAs may affect the development of A. c. cerana workers' midguts by targeting miR-6001-y. Finally, four randomly selected DEcircRNAs were verified via RT-qPCR, confirming the reliability of our sequencing data.Conclusion: This is the first systematic investigation of circRNAs and their correspond...

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Section: Validation Of Decircrnas In the A C Cerana Worker's Midgutmentioning

confidence: 99%

Section: Pcr Confirmation Of Novel Circrna With Convergent and Divergmentioning

confidence: 99%

Section: Real Time Quantitative Pcr Validation Of Decircrnamentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut ofApis cerana ceranaworkers

Chen

et al. 2019

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Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midguts of eastern honeybee workers

Chen

et al. 2019

Appl Microbiol Biotechnol

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Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection

Guo,

Zhang,

Zang

et al. 2024

Appl Microbiol Biotechnol

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Non-coding RNA (ncRNA) plays a vital part in the regulation of immune responses, growth, and development in plants and animals. Here, the identification, characteristic analysis, and molecular verification of circRNAs in Apis cerana cerana worker larval guts were conducted, followed by in-depth investigation of the expression pattern of larval circRNAs during Ascosphaera apis infection and exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 3178 circRNAs in the larval guts of A. c. cerana were identified, with a length distribution ranging from 15 to 96,007 nt. Additionally, 155, 95, and 86 DEcircRNAs were identified in the in the 4-, 5-, and 6-day-old larval guts following A. apis infection. These DEcircRNAs were predicted to target 29, 25, and 18 parental genes relevant to 12, 20, and 17 GO terms as well as 144, 114, and 61 KEGG pathways, including 5 cellular and 4 humoral immune pathways. Complex competing endogenous RNA (ceRNA) regulatory networks were detected as being formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The target DEmRNAs were engaged in 36, 47, and 47 GO terms as well as 331, 332, and 331 pathways, including 6 cellular and 6 humoral immune pathways. Further, 19 DEcircRNAs, 5 DEmiRNAs, and 3 mRNAs were included in the sub-networks relative to 3 antioxidant enzymes. Finally, back-splicing sites within 15 circRNAs and the difference in the 15 DEcircRNAs’ expression between uninoculated and A. apis–inoculated larval guts were confirmed based on molecular methods. These findings not only enrich our understanding of bee host–fungal pathogen interactions but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. c. cerana larvae against A. apis invasion. Key points • The expression pattern of circRNAs was altered in the A. cerana worker larval guts following A. apis infection. • Back-splicing sites within 15 A. cerana circRNAs were verified using molecular approaches. DEcircRNAs potentially modulated immune responses and antioxidant enzymes in A. apis–challenged host guts.

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Systematic investigation of circular RNAs in Ascosphaera apis, a fungal pathogen of honeybee larvae

Cited by 24 publications

References 43 publications

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut ofApis cerana ceranaworkers

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midgut ofApis cerana ceranaworkers

Systematic identification of circular RNAs and corresponding regulatory networks unveil their potential roles in the midguts of eastern honeybee workers

Dynamics and regulatory role of circRNAs in Asian honey bee larvae following fungal infection

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