ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

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.