Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression
Abstract Background Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions i...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-12-01
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| Series: | Genome Medicine |
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| Online Access: | https://doi.org/10.1186/s13073-020-00812-8 |
| _version_ | 1819203363287334912 |
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| author | Trine Line Hauge Okholm Shashank Sathe Samuel S. Park Andreas Bjerregaard Kamstrup Asta Mannstaedt Rasmussen Archana Shankar Zong Ming Chua Niels Fristrup Morten Muhlig Nielsen Søren Vang Lars Dyrskjøt Stefan Aigner Christian Kroun Damgaard Gene W. Yeo Jakob Skou Pedersen |
| author_facet | Trine Line Hauge Okholm Shashank Sathe Samuel S. Park Andreas Bjerregaard Kamstrup Asta Mannstaedt Rasmussen Archana Shankar Zong Ming Chua Niels Fristrup Morten Muhlig Nielsen Søren Vang Lars Dyrskjøt Stefan Aigner Christian Kroun Damgaard Gene W. Yeo Jakob Skou Pedersen |
| author_sort | Trine Line Hauge Okholm |
| collection | DOAJ |
| description | Abstract Background Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts. Methods We conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq. Results We generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53. Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients. Conclusions Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis. |
| first_indexed | 2024-12-23T04:18:43Z |
| format | Article |
| id | doaj.art-07a2b5a8c7034ce9ae1a8efb8d815836 |
| institution | Directory Open Access Journal |
| issn | 1756-994X |
| language | English |
| last_indexed | 2024-12-23T04:18:43Z |
| publishDate | 2020-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Medicine |
| spelling | doaj.art-07a2b5a8c7034ce9ae1a8efb8d8158362022-12-21T18:00:18ZengBMCGenome Medicine1756-994X2020-12-0112112210.1186/s13073-020-00812-8Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expressionTrine Line Hauge Okholm0Shashank Sathe1Samuel S. Park2Andreas Bjerregaard Kamstrup3Asta Mannstaedt Rasmussen4Archana Shankar5Zong Ming Chua6Niels Fristrup7Morten Muhlig Nielsen8Søren Vang9Lars Dyrskjøt10Stefan Aigner11Christian Kroun Damgaard12Gene W. Yeo13Jakob Skou Pedersen14Department of Molecular Medicine (MOMA), Aarhus University HospitalDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Molecular Biology and Genetics, Aarhus UniversityDepartment of Molecular Medicine (MOMA), Aarhus University HospitalDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Oncology, Aarhus University HospitalDepartment of Molecular Medicine (MOMA), Aarhus University HospitalDepartment of Molecular Medicine (MOMA), Aarhus University HospitalDepartment of Molecular Medicine (MOMA), Aarhus University HospitalDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Molecular Biology and Genetics, Aarhus UniversityDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Molecular Medicine (MOMA), Aarhus University HospitalAbstract Background Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions in different biological contexts. Methods We conduct an extensive screen of circRNA-RBP interactions in the ENCODE cell lines HepG2 and K562. We profile circRNAs in deep-sequenced total RNA samples and analyze circRNA-RBP interactions using a large set of eCLIP data with binding sites of 150 RBPs. We validate interactions for select circRNAs and RBPs by performing RNA immunoprecipitation and functionally characterize our most interesting candidates by conducting knockdown studies followed by RNA-Seq. Results We generate a comprehensive catalog of circRNA-RBP interactions in HepG2 and K562 cells. We show that KHSRP binding sites are enriched in flanking introns of circRNAs and that KHSRP depletion affects circRNA biogenesis. We identify circRNAs that are highly covered by RBP binding sites and experimentally validate individual circRNA-RBP interactions. We show that circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, is almost completely covered with GRWD1 binding sites in HepG2 cells, and that circCDYL depletion counteracts the effect of GRWD1 depletion. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g., TP53. Finally, we show that elevated levels of circCDYL are associated with overall survival of bladder cancer patients. Conclusions Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.https://doi.org/10.1186/s13073-020-00812-8Circular RNAsRNA-binding proteinsRBP spongescircCDYLBladder cancerTumorigenesis |
| spellingShingle | Trine Line Hauge Okholm Shashank Sathe Samuel S. Park Andreas Bjerregaard Kamstrup Asta Mannstaedt Rasmussen Archana Shankar Zong Ming Chua Niels Fristrup Morten Muhlig Nielsen Søren Vang Lars Dyrskjøt Stefan Aigner Christian Kroun Damgaard Gene W. Yeo Jakob Skou Pedersen Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression Genome Medicine Circular RNAs RNA-binding proteins RBP sponges circCDYL Bladder cancer Tumorigenesis |
| title | Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression |
| title_full | Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression |
| title_fullStr | Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression |
| title_full_unstemmed | Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression |
| title_short | Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression |
| title_sort | transcriptome wide profiles of circular rna and rna binding protein interactions reveal effects on circular rna biogenesis and cancer pathway expression |
| topic | Circular RNAs RNA-binding proteins RBP sponges circCDYL Bladder cancer Tumorigenesis |
| url | https://doi.org/10.1186/s13073-020-00812-8 |
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