Journal
BMC GENOMICS
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s12864-020-07289-0
Keywords
Mesenchymal stem cell; Transcriptomics; Long non-coding RNA; RNAseq; NGS analysis; Bioinformatics
Funding
- Agence Nationale de la recherche [18-CE45-0020-02, ANR-10-INBS-09]
- Canceropole Grand-Sud-Ouest Trans-kmer project [2017-EM24]
Ask authors/readers for more resources
The study developed a dedicated bioinformatics pipeline to identify unannotated lncRNAs in MSCs, highlighting novel lncRNAs with high cell specificity. Through original and efficient methods for functional prediction, it was demonstrated that each candidate represents a specific state of MSC biology. The approach showed potential for utilizing lncRNAs as cell markers and suggested promising directions for future experimental investigations.
Background The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function. Therefore, we tested the biomarker potential of lncRNAs on Mesenchymal Stem Cells (MSCs), a complex type of adult multipotent stem cells of diverse tissue origins, that is frequently used in clinics but which is lacking extensive characterization. Results We developed a dedicated bioinformatics pipeline for the purpose of building a cell-specific catalogue of unannotated lncRNAs. The pipeline performs ab initio transcript identification, pseudoalignment and uses new methodologies such as a specific k-mer approach for naive quantification of expression in numerous RNAseq data. We next applied it on MSCs, and our pipeline was able to highlight novel lncRNAs with high cell specificity. Furthermore, with original and efficient approaches for functional prediction, we demonstrated that each candidate represents one specific state of MSCs biology. Conclusions We showed that our approach can be employed to harness lncRNAs as cell markers. More specifically, our results suggest different candidates as potential actors in MSCs biology and propose promising directions for future experimental investigations.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available