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ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data
Milana Frenkel-Morgenstern1, Alessandro Gorohovski, Vincent Lacroix
1Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
Abstract:
Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes. The ChiTaRS database of Chimeric Transcripts and RNA-Sequencing data (http://chitars.bioinfo.cnio.es/) collects more than 16 000 chimeric RNAs from humans, mice and fruit flies, 233 chimeras confirmed by RNA-seq reads and ∼2000 cancer breakpoints. The database indicates the expression and tissue specificity of these chimeras, as confirmed by RNA-seq data, and it includes mass spectrometry results for some human entries at their junctions. Moreover, the database has advanced features to analyze junction consistency and to rank chimeras based on the evidence of repeated junction sites. Finally, 'Junction Search' screens through the RNA-seq reads found at the chimeras' junction sites to identify putative junctions in novel sequences entered by users. Thus, ChiTaRS is an extensive catalog of human, mouse and fruit fly chimeras that will extend our understanding of the evolution of chimeric transcripts in eukaryotes and can be advantageous in the analysis of human cancer breakpoints.
Insights
Chimeric RNAs, found in cancers and various organisms, can lead to functional proteins and disease. The ChiTaRS database catalogs these chimeric transcripts, aiding cancer breakpoint analysis and understanding eukaryotic evolution.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Chimeric RNAs, formed from multiple transcripts, are implicated in various cancers and can influence disease phenotypes.
- Expressed Sequence Tags (ESTs) from diverse organisms have revealed the presence of chimeric RNAs.
- Understanding chimeric RNA formation and function is crucial for cancer research.
Purpose of the Study:
- To establish the ChiTaRS database, a comprehensive resource for chimeric RNAs and RNA-sequencing data.
- To provide tools for analyzing chimeric RNA expression, tissue specificity, and junction consistency.
- To facilitate the identification of novel chimeric junctions and aid in cancer breakpoint analysis.
Main Methods:
- Compilation of over 16,000 chimeric RNAs from humans, mice, and fruit flies.
- Integration of RNA-sequencing data to confirm chimeric transcripts and identify cancer breakpoints.
- Inclusion of mass spectrometry data for human chimeric RNA junctions.
- Development of advanced analytical features for junction consistency and ranking.
- Implementation of a 'Junction Search' tool for novel sequence analysis.
Main Results:
- The ChiTaRS database contains extensive data on chimeric RNAs across multiple species.
- Confirmed chimeric RNAs and cancer breakpoints are cataloged with supporting RNA-seq evidence.
- Expression and tissue specificity data are available for numerous chimeric RNAs.
- Advanced analysis tools enable robust evaluation of chimeric RNA evidence.
Conclusions:
- ChiTaRS serves as an extensive catalog of chimeric RNAs in humans, mice, and fruit flies.
- The database enhances understanding of chimeric transcript evolution in eukaryotes.
- ChiTaRS is a valuable resource for analyzing human cancer breakpoints and identifying functional chimeric RNAs.
