Comprehensive Transcriptome Landscape And Complex Alternative Splicing Regulation In Mouse Based On Large Scale RNA-Seq Dataset

As one of the most important model organism, mouse (Mus musculus) plays an important role in biomedical researches, which is widely used in genetic research, drug toxicity testing, and oncological study for its short life cycle, reproduction ability and high similarity to human in terms of physiology, anatomy, and genetics. However, the transcriptome of mouse is not yet well annotated, although great efforts have been made to improve it. Here, we investigated mouse transcriptome utilizing RNA-Seq data generated from18mouse normal tissues. As a result,34,944transcripts from32433novel transcribed regions (NTRs) located in intronic or intergenic regions were assembled. Abundant novel alternative splicing events underlying known or unknown genes were identified. More specifically,6,760potential cassette exons (PCEs) were identified, whose conservation in flanking intronic regions adjacent to PCEs are significantly higher than that of non-cassette exons. These regions may act as splicing signal sequences recognized by spliceosome. Besides, we showed the overall view of gene expression and alternative slicing across diverse tissues examined. We noted that the brain, as the most sophisticated organ in vivo, had the largest number of tissue-enriched genes and the most special way of alternative splicing. Meanwhile, the result also shows certain types of alternative splicing (AS) events play different roles in isoform-level diversity and regulation.