Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq
Recently, circular RNAs (circRNAs) have been extensively studied in animals and plants. circRNAs are generated by backsplicing from the same linear transcripts that are canonically spliced to produce, for example, mature mRNAs. circRNAs exhibit tissue-specific expression and are potentially involved...
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| Format: | Article |
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.875805/full |
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| author | Isabel S. Naarmann-de Vries Isabel S. Naarmann-de Vries Jessica Eschenbach Sarah Schudy Sarah Schudy Benjamin Meder Benjamin Meder Benjamin Meder Christoph Dieterich Christoph Dieterich |
| author_facet | Isabel S. Naarmann-de Vries Isabel S. Naarmann-de Vries Jessica Eschenbach Sarah Schudy Sarah Schudy Benjamin Meder Benjamin Meder Benjamin Meder Christoph Dieterich Christoph Dieterich |
| author_sort | Isabel S. Naarmann-de Vries |
| collection | DOAJ |
| description | Recently, circular RNAs (circRNAs) have been extensively studied in animals and plants. circRNAs are generated by backsplicing from the same linear transcripts that are canonically spliced to produce, for example, mature mRNAs. circRNAs exhibit tissue-specific expression and are potentially involved in many diseases, among them cardiovascular diseases. The comprehensive analysis of circRNA expression patterns across larger patient cohorts requires a streamlined and cost-effective workflow designed to meet small input requirements. In this article, we present Lexo-circSeq, a targeted RNA sequencing approach that can profile up to 110 circRNAs and their corresponding linear transcripts in one experiment. We established Lexo-circSeq employing total human heart RNA and show that our protocol can detect depletion of a specific circRNA in hiPSC-derived cardiomyocytes. Finally, Lexo-circSeq was applied to biopsies from patients diagnosed with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), respectively. Interestingly, our results indicate that circular-to-linear-ratios for circSLC8A1 and circRBM33 are deregulated in cardiomyopathy. |
| first_indexed | 2024-04-12T13:19:07Z |
| format | Article |
| id | doaj.art-fa90a8c89519419b96df97d6cfb3e016 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-12T13:19:07Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-fa90a8c89519419b96df97d6cfb3e0162022-12-22T03:31:35ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-06-01910.3389/fmolb.2022.875805875805Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeqIsabel S. Naarmann-de Vries0Isabel S. Naarmann-de Vries1Jessica Eschenbach2Sarah Schudy3Sarah Schudy4Benjamin Meder5Benjamin Meder6Benjamin Meder7Christoph Dieterich8Christoph Dieterich9Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, GermanyGerman Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, GermanyDepartment of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, GermanyGerman Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, GermanyDepartment of Internal Medicine III, Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, GermanyGerman Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, GermanyDepartment of Internal Medicine III, Institute for Cardiomyopathies, University Hospital Heidelberg, Heidelberg, GermanyStanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, United StatesDepartment of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, GermanyGerman Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, GermanyRecently, circular RNAs (circRNAs) have been extensively studied in animals and plants. circRNAs are generated by backsplicing from the same linear transcripts that are canonically spliced to produce, for example, mature mRNAs. circRNAs exhibit tissue-specific expression and are potentially involved in many diseases, among them cardiovascular diseases. The comprehensive analysis of circRNA expression patterns across larger patient cohorts requires a streamlined and cost-effective workflow designed to meet small input requirements. In this article, we present Lexo-circSeq, a targeted RNA sequencing approach that can profile up to 110 circRNAs and their corresponding linear transcripts in one experiment. We established Lexo-circSeq employing total human heart RNA and show that our protocol can detect depletion of a specific circRNA in hiPSC-derived cardiomyocytes. Finally, Lexo-circSeq was applied to biopsies from patients diagnosed with dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), respectively. Interestingly, our results indicate that circular-to-linear-ratios for circSLC8A1 and circRBM33 are deregulated in cardiomyopathy.https://www.frontiersin.org/articles/10.3389/fmolb.2022.875805/fullcircRNAcardiomyopathySLC8A1RBM33RNA-seq |
| spellingShingle | Isabel S. Naarmann-de Vries Isabel S. Naarmann-de Vries Jessica Eschenbach Sarah Schudy Sarah Schudy Benjamin Meder Benjamin Meder Benjamin Meder Christoph Dieterich Christoph Dieterich Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq Frontiers in Molecular Biosciences circRNA cardiomyopathy SLC8A1 RBM33 RNA-seq |
| title | Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq |
| title_full | Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq |
| title_fullStr | Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq |
| title_full_unstemmed | Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq |
| title_short | Targeted Analysis of circRNA Expression in Patient Samples by Lexo-circSeq |
| title_sort | targeted analysis of circrna expression in patient samples by lexo circseq |
| topic | circRNA cardiomyopathy SLC8A1 RBM33 RNA-seq |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.875805/full |
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