title: Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells.
abstract: Alternative RNA splicing greatly increases proteome diversity, and the possibility of studying genome-wide alternative splicing (AS) events becomes available with the advent of high-throughput genomics tools devoted to this issue. Kaposi's sarcoma associated herpesvirus (KSHV) is the etiological agent of KS, a tumor of lymphatic endothelial cell (LEC) lineage, but little is known about the AS variations induced by KSHV. We analyzed KSHV-controlled AS using high-density microarrays capable of detecting all exons in the human genome. Splicing variants and altered exon-intron usage in infected LEC were found, and these correlated with protein domain modification. The different 3'-UTR used in new transcripts also help isoforms to escape microRNA-mediated surveillance. Exome-level analysis further revealed information that cannot be disclosed using classical gene-level profiling: a significant exon usage difference existed between LEC and CD34(+) precursor cells, and KSHV infection resulted in LEC-to-precursor, dedifferentiation-like exon level reprogramming. Our results demonstrate the application of exon arrays in systems biology research, and suggest the regulatory effects of AS in endothelial cells are far more complex than previously observed. This extra layer of molecular diversity helps to account for various aspects of endothelial biology, KSHV life cycle and disease pathogenesis that until now have been unexplored.
authors.affiliation: Institute of Microbiology and Immunology, National Yang-Ming University, 11221, Taipei, Taiwan.
authors.forename: Ting-Yu
authors.initials: TY
authors.lastname: Chang
authors.forename: Yu-Hsuan
authors.initials: YH
authors.lastname: Wu
authors.forename: Cheng-Chung
authors.initials: CC
authors.lastname: Cheng
authors.forename: Hsei-Wei
authors.initials: HW
authors.lastname: Wang
mesh_terms: D017398:Alternative Splicing; D020816:Amino Acid Motifs; D001665:Binding Sites; D054337:Cell Dedifferentiation; D002478:Cells, Cultured; D042783:Endothelial Cells / Q000378:metabolism / Q000821:virology*; D004729:Endothelium, Lymphatic / Q000166:cytology / Q000378:metabolism / Q000821:virology*; D053263:Gene Regulatory Networks; D019288:Herpesvirus 8, Human / Q000502:physiology*; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D020033:Protein Isoforms / Q000737:chemistry; D017434:Protein Structure, Tertiary; D049490:Systems Biology
chemical_list: D035683:MicroRNAs; D020033:Protein Isoforms