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Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps

Circular RNAs (circRNAs) have gained recent attraction due to their functional versatility and particular structure connected to human diseases. Current investigations are focused on the interplay between their ability to sponge smaller species of RNAs, such as microRNAs (miRNAs), thus influencing t...

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Autores principales: Drula, Rares, Braicu, Cornelia, Chira, Sergiu, Berindan-Neagoe, Ioana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10056686/
https://www.ncbi.nlm.nih.gov/pubmed/36982797
http://dx.doi.org/10.3390/ijms24065721
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author Drula, Rares
Braicu, Cornelia
Chira, Sergiu
Berindan-Neagoe, Ioana
author_facet Drula, Rares
Braicu, Cornelia
Chira, Sergiu
Berindan-Neagoe, Ioana
author_sort Drula, Rares
collection PubMed
description Circular RNAs (circRNAs) have gained recent attraction due to their functional versatility and particular structure connected to human diseases. Current investigations are focused on the interplay between their ability to sponge smaller species of RNAs, such as microRNAs (miRNAs), thus influencing their regulatory activity on gene expression and protein templates. Therefore, their reported implication in various biological processes axis has resulted in an accumulating number of studies. While the testing and annotation methods of novel circular transcripts are still under development, there is still a plethora of transcript candidates suitable for investigation in human disease. The discordance in the literature regarding the approaches used in circRNAs quantification and validation methods, especially regarding qRT-PCR, the current golden standard procedure, leads to high result variability and undermines the replicability of the studies. Therefore, our study will offer several valuable insights into bioinformatic data for experimental design for circRNA investigation and in vitro aspects. Specifically, we will highlight key aspects such as circRNA database annotation divergent primer design and several processing steps, such as RNAse R treatment optimization and circRNA enrichment assessment. Additionally, we will provide insights into the exploration of circRNA-miRNA interactions, a prerequisite for further functional investigations. With this, we aim to contribute to the methodological consensus in a currently expanding field with possible implications for assessing therapeutic targets and biomarker discovery.
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spelling pubmed-100566862023-03-30 Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps Drula, Rares Braicu, Cornelia Chira, Sergiu Berindan-Neagoe, Ioana Int J Mol Sci Article Circular RNAs (circRNAs) have gained recent attraction due to their functional versatility and particular structure connected to human diseases. Current investigations are focused on the interplay between their ability to sponge smaller species of RNAs, such as microRNAs (miRNAs), thus influencing their regulatory activity on gene expression and protein templates. Therefore, their reported implication in various biological processes axis has resulted in an accumulating number of studies. While the testing and annotation methods of novel circular transcripts are still under development, there is still a plethora of transcript candidates suitable for investigation in human disease. The discordance in the literature regarding the approaches used in circRNAs quantification and validation methods, especially regarding qRT-PCR, the current golden standard procedure, leads to high result variability and undermines the replicability of the studies. Therefore, our study will offer several valuable insights into bioinformatic data for experimental design for circRNA investigation and in vitro aspects. Specifically, we will highlight key aspects such as circRNA database annotation divergent primer design and several processing steps, such as RNAse R treatment optimization and circRNA enrichment assessment. Additionally, we will provide insights into the exploration of circRNA-miRNA interactions, a prerequisite for further functional investigations. With this, we aim to contribute to the methodological consensus in a currently expanding field with possible implications for assessing therapeutic targets and biomarker discovery. MDPI 2023-03-16 /pmc/articles/PMC10056686/ /pubmed/36982797 http://dx.doi.org/10.3390/ijms24065721 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Drula, Rares
Braicu, Cornelia
Chira, Sergiu
Berindan-Neagoe, Ioana
Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title_full Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title_fullStr Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title_full_unstemmed Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title_short Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps
title_sort investigating circular rnas using qrt-pcr; roundup of optimization and processing steps
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10056686/
https://www.ncbi.nlm.nih.gov/pubmed/36982797
http://dx.doi.org/10.3390/ijms24065721
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