CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements

Combinatorial Pattern of Histone Modifications in Exon Skipping Event

Histone modifications are associated with alternative splicing. It has been suggested that histone modifications act in combinational patterns in gene expression regulation. However, how they interact with each other and what is their casual relationships in the process of RNA splicing remain unclear. In this study, the combinatorial patterns of 38 kinds of histone modifications in the exon skipping event of the CD4⁺ T cell were analyzed by constructing Bayesian networks. Distinct combinatorial patterns of histone modifications that illustrating their casual relationships were observed in excluded/included exons and the surrounding intronic regions. The Bayesian networks also indicate that some histone modifications directly correlate with RNA splicing. We anticipate that this work could provide novel insights into the effects of histone modifications on RNA splicing regulation.

Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data

Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs. In our pipeline, we utilize the DEXSeq package along with our previously reported algorithms. Utilizing the publicly available RNA-Seq data set from the Human BodyMap project, we identified 28,100 differentially used exons across the four tissues. We identified tissue-specific exonic splicing enhancers that overlap with various previously published experimental and computational databases. A complicated exonic enhancer regulatory network was revealed, where multiple exonic enhancers were found across multiple tissues while some were found only in specific tissues. Putative combinatorial exonic enhancers and silencers were discovered as well, which may be responsible for exon inclusion or exclusion across tissues. Some of the exonic enhancers are found to be co-occurring with multiple exonic silencers and vice versa, which demonstrates a complicated relationship between tissue-specific exonic enhancers and silencers.