NDLI: Splicing complexity as a pivotal feature of alternative exons in mammalian species

Content Provider	Springer Nature : BioMed Central
Author	Zhao, Feiyang Yan, Yubin Wang, Yaxi Liu, Yuan Yang, Ruolin
Abstract	Background As a significant process of post-transcriptional gene expression regulation in eukaryotic cells, alternative splicing (AS) of exons greatly contributes to the complexity of the transcriptome and indirectly enriches the protein repertoires. A large number of studies have focused on the splicing inclusion of alternative exons and have revealed the roles of AS in organ development and maturation. Notably, AS takes place through a change in the relative abundance of the transcript isoforms produced by a single gene, meaning that exons can have complex splicing patterns. However, the commonly used percent spliced-in (Ψ) values only define the usage rate of exons, but lose information about the complexity of exons’ linkage pattern. To date, the extent and functional consequence of splicing complexity of alternative exons in development and evolution is poorly understood. Results By comparing splicing complexity of exons in six tissues (brain, cerebellum, heart, liver, kidney, and testis) from six mammalian species (human, chimpanzee, gorilla, macaque, mouse, opossum) and an outgroup species (chicken), we revealed that exons with high splicing complexity are prevalent in mammals and are closely related to features of genes. Using traditional machine learning and deep learning methods, we found that the splicing complexity of exons can be moderately predicted with features derived from exons, among which length of flanking exons and splicing strength of downstream/upstream splice sites are top predictors. Comparative analysis among human, chimpanzee, gorilla, macaque, and mouse revealed that, alternative exons tend to evolve to an increased level of splicing complexity and higher tissue specificity in splicing complexity. During organ development, not only developmentally regulated exons, but also 10–15% of non-developmentally regulated exons show dynamic splicing complexity. Conclusions Our analysis revealed that splicing complexity is an important metric to characterize the splicing dynamics of alternative exons during the development and evolution of mammals.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-023-09247-y.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-023-09247-y
Journal	BMC Genomics
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-04-12
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Alternative splicing Splicing complexity Machine learning Development and evolution
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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