1
|
Morlion A, Everaert C, Nuytens J, Hulstaert E, Vandesompele J, Mestdagh P. Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA Biol 2021; 18:215-222. [PMID: 34470578 PMCID: PMC8682977 DOI: 10.1080/15476286.2021.1971438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.
Collapse
Affiliation(s)
- Annelien Morlion
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Celine Everaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Justine Nuytens
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Hulstaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| |
Collapse
|