Differential splicing across immune system lineages

Abstract

Alternative splicing (AS) allows increased diversity and orthogonal regulation of the transcriptional products of mammalian genomes. To assess the distribution and variation of alternative splicing across cell lineages of the immune system, we comprehensively analyzed RNA sequencing and microarray data generated by the Immunological Genome Project Consortium. AS is pervasive: 60% of genes showed frequent AS isoforms in T or B lymphocytes, with 7,599 previously unreported isoforms. Distinct cell specificity was observed, with differential exon skipping in 5% of genes otherwise coexpressed in both B and T cells. The distribution of isoforms was mostly all or none, suggesting on/off switching as a frequent mode of AS regulation in lymphocytes. From the identification of differential exon use in the microarray data, clustering of exon inclusion/exclusion patterns across all Immunological Genome Project cell types showed that ∼70% of AS exons are distributed along a common pattern linked to lineage differentiation and cell cycling. Other AS events distinguished myeloid from lymphoid cells or affected only a small set of exons without clear lineage specificity (e.g., Ptprc). Computational analysis predicted specific associations between AS exons and splicing regulators, which were verified by detection of the hnRPLL/ Ptprc connection.A lternative splicing (AS), the process of selectively including or removing exons to create a variety of transcripts from the same pre-mRNA, plays an important role in amplifying the diversity and flexibility of genome-encoded molecules (1, 2). AS can result in different protein isoforms or generate mRNAs of identical coding sequence but varying in their stability, localization, susceptibility to translational control, or microRNA regulation. AS is frequent and ubiquitous, affecting 55-95% of multiexon genes in mammals in different estimates (3-6). It is involved in a wide range of biological phenomena, ranging from sex determination to apoptosis or tumor formation. It also allows evolutionary tinkering with transcript structure and gradual transitions in gene function (7).Splicing events are overrepresented in genes involved in signaling and transcriptional regulation (receptors, signaling transduction, and transcription factors) and immune and nervous system processes. It has been hypothesized that alternative splicing is particularly valuable in complex systems, where information is processed differently at different times (immune response) or fine-tuning of signal integration is important (5). In the immune system, the first instance of AS recognized was the now textbook case of differential processing of primary Ig transcripts generating either a membrane receptor in naïve B cells or a secreted protein after antigen-induced differentiation (8). Other notable examples are the splicing of transcripts encoding adhesion molecules such as PECAM1 or CD44, which modulate cell-stroma interactions, or the extracellular domain of the coinhibitory molecule CTLA4 (9). A particularly well-studie...

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