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CirComPara: A Multi‐Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA‐seq Data

Authors :
Enrico Gaffo
Annagiulia Bonizzato
Geertruy te Kronnie
Stefania Bortoluzzi
Source :
Non-Coding RNA, Vol 3, Iss 1, p 8 (2017)
Publication Year :
2017
Publisher :
MDPI AG, 2017.

Abstract

Circular RNAs (circRNAs) are generated by backsplicing of immature RNA forming covalently closed loops of intron/exon RNA molecules. Pervasiveness, evolutionary conservation, massive and regulated expression, and posttranscriptional regulatory roles of circRNAs in eukaryotes have been appreciated and described only recently. Moreover, being easily detectable disease markers, circRNAs undoubtedly represent a molecular class with high bearing on molecular pathobiology. CircRNAs can be detected from RNAseq data using appropriate computational methods to identify the sequence reads spanning backsplice junctions that do not colinearly map to the reference genome. To this end, several programs were developed and critical assessment of various strategies and tools suggested the combination of at least two methods as good practice to guarantee robust circRNA detection. Here,we present CirComPara (http://github.com/egaffo/CirComPara), an automated bioinformatics pipeline, to detect, quantify and annotate circRNAs from RNAseq data using in parallel four different methods for backsplice identification. CirComPara also provides quantification of linear RNAs and gene expression, ultimately comparing and correlating circRNA and gene/transcript expression level. We applied our method to RNAseqdata of monocyte and macrophage samples in relation to haploinsufficiency of the RNAbinding splicing factor Quaking (QKI). The biological relevance of the results, in terms of number, types and variations of circRNAs expressed, illustrates CirComPara potential to enlarge the knowledge of the transcriptome, adding details on the circRNAome, and facilitating further computational and experimental studies.

Details

Language :
English
ISSN :
2311553X
Volume :
3
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Non-Coding RNA
Publication Type :
Academic Journal
Accession number :
edsdoj.1a9e35dae5dc472d9b811e7f830dca25
Document Type :
article
Full Text :
https://doi.org/10.3390/ncrna3010008