ArticleMethods in molecular biology (Clifton, N.J.)2026
Identification of Cross-Strand Chimeric RNAs with cscMap.
Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Chimeric RNAs could be originated from chromosome rearrangements at the DNA level or from posttranscriptional RNA fusion events, such as trans-spicing between distal genes and cis-splicing between adjacent genes. In addition to the mechanisms above, we have identified a new type of chimeric RNA, cross-strand chimeric RNA (cscRNA), which are fusion products of the transcripts encoded by the two opposite DNA strands. In this chapter, we present the workflow of cscMap, a specialized bioinformatics pipeline designed for de novo identification of the cscRNAs, directly from RNA deep sequencing data without prior annotations. cscMap employs a series of meticulous measurements to ensure high accuracy in detecting cross-strand junction events. This approach and the cscRNA species could serve as a valuable resource for further exploration of the origins and functions of cscRNAs.
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