ChiTaRS 5.0: The comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps

Deepak Balamurali, Alessandro Gorohovski, Rajesh Detroja, Vikrant Palande, Dorith Raviv-Shay, Milana Frenkel-Morgenstern

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

Chimeric RNA transcripts are formed when exons from two genes fuse together, often due to chromosomal translocations, transcriptional errors or trans-splicing effect. While these chimeric RNAs produce functional proteins only in certain cases, they play a significant role in disease phenotyping and progression. ChiTaRS 5.0 (http://chitars.md.biu.ac.il/) is the latest and most comprehensive chimeric transcript repository, with 111 582 annotated entries from eight species, including 23 167 known human cancer breakpoints. The database includes unique information correlating chimeric breakpoints with 3D chromatin contact maps, generated from public datasets of chromosome conformation capture techniques (Hi-C). In this update, we have added curated information on druggable fusion targets matched with chimeric breakpoints, which are applicable to precision medicine in cancers. The introduction of a new section that lists chimeric RNAs in various cell-lines is another salient feature. Finally, using text-mining techniques, novel chimeras in Alzheimer's disease, schizophrenia, dyslexia and other diseases were collected in ChiTaRS. Thus, this improved version is an extensive catalogue of chimeras from multiple species. It extends our understanding of the evolution of chimeric transcripts in eukaryotes and contributes to the analysis of 3D genome conformational changes and the functional role of chimeras in the etiopathogenesis of cancers and other complex diseases.

Original languageEnglish
Pages (from-to)D825-D834
JournalNucleic Acids Research
Volume48
Issue numberD1
DOIs
StatePublished - 8 Jan 2020

Bibliographical note

Funding Information:
Israel Cancer Association (ICA) [204562]; Israel Innovation Authority ‘Kamin’ [66824 to M.F-M.]; M.F-M. is a board member of the Data Science Institute, and a member of the Dangoor Personalized Medicine Institute at the Bar-Ilan University. Funding for open access charge: Israel Cancer Association (ICA) [204562]; Israel Innovation Authority ‘Kamin’ [66824 to M.F-M.]. Conflict of interest statement. None declared.

Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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