Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis
Abstract Background Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. Results In this stu...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s12915-025-02233-8 |
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| author | Mohan Wang Shanshan Zheng Yan Zhang Jingwen Zhang Fuming Lai Cong Zhou Qiangwei Zhou Xingwang Li Guoliang Li |
| author_facet | Mohan Wang Shanshan Zheng Yan Zhang Jingwen Zhang Fuming Lai Cong Zhou Qiangwei Zhou Xingwang Li Guoliang Li |
| author_sort | Mohan Wang |
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| description | Abstract Background Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. Results In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation. Conclusions In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia. Graphical Abstract |
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| publishDate | 2025-05-01 |
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| spelling | doaj-art-024fbaefd2324d01b806b09005cc2aed2025-08-20T02:25:17ZengBMCBMC Biology1741-70072025-05-0123111710.1186/s12915-025-02233-8Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesisMohan Wang0Shanshan Zheng1Yan Zhang2Jingwen Zhang3Fuming Lai4Cong Zhou5Qiangwei Zhou6Xingwang Li7Guoliang Li8National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityAgricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityAgricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming Technology for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural UniversityAbstract Background Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. Results In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation. Conclusions In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia. Graphical Abstracthttps://doi.org/10.1186/s12915-025-02233-8Circular RNAsRNA binding proteinsPTBP1TranscriptomeBiogenesis |
| spellingShingle | Mohan Wang Shanshan Zheng Yan Zhang Jingwen Zhang Fuming Lai Cong Zhou Qiangwei Zhou Xingwang Li Guoliang Li Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis BMC Biology Circular RNAs RNA binding proteins PTBP1 Transcriptome Biogenesis |
| title | Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis |
| title_full | Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis |
| title_fullStr | Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis |
| title_full_unstemmed | Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis |
| title_short | Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis |
| title_sort | transcriptome analysis reveals ptbp1 as a key regulator of circrna biogenesis |
| topic | Circular RNAs RNA binding proteins PTBP1 Transcriptome Biogenesis |
| url | https://doi.org/10.1186/s12915-025-02233-8 |
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