title: Comprehensive analysis of alternative splicing and functionality in neuronal differentiation of P19 cells.
abstract: BACKGROUND
  Alternative splicing, which produces multiple mRNAs from a single gene, occurs in most human genes and contributes to protein diversity. Many alternative isoforms are expressed in a spatio-temporal manner, and function in diverse processes, including in the neural system.
  
  
  RESULTS
  The purpose of the present study was to comprehensively investigate neural-splicing using P19 cells. GeneChip Exon Array analysis was performed using total RNAs purified from cells during neuronal cell differentiation. To efficiently and readily extract the alternative exon candidates, 9 filtering conditions were prepared, yielding 262 candidate exons (236 genes). Semiquantitative RT-PCR results in 30 randomly selected candidates suggested that 87% of the candidates were differentially alternatively spliced in neuronal cells compared to undifferentiated cells. Gene ontology and pathway analyses suggested that many of the candidate genes were associated with neural events. Together with 66 genes whose functions in neural cells or organs were reported previously, 47 candidate genes were found to be linked to 189 events in the gene-level profile of neural differentiation. By text-mining for the alternative isoform, distinct functions of the isoforms of 9 candidate genes indicated by the result of Exon Array were confirmed.
  
  
  CONCLUSIONS
  Alternative exons were successfully extracted. Results from the informatics analyses suggested that neural events were primarily governed by genes whose expression was increased and whose transcripts were differentially alternatively spliced in the neuronal cells. In addition to known functions in neural cells or organs, the uninvestigated alternative splicing events of 11 genes among 47 candidate genes suggested that cell cycle events are also potentially important. These genes may help researchers to differentiate the roles of alternative splicing in cell differentiation and cell proliferation.
authors.affiliation: Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan. suzuki-h@jaist.ac.jp
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Suzuki
authors.forename: Ken
authors.initials: K
authors.lastname: Osaki
authors.forename: Kaori
authors.initials: K
authors.lastname: Sano
authors.forename: A H M Khurshid
authors.initials: AH
authors.lastname: Alam
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Yasuhito
authors.initials: Y
authors.lastname: Ishigaki
authors.forename: Kozo
authors.initials: K
authors.lastname: Kawahara
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Tsukahara
mesh_terms: D017398:Alternative Splicing / Q000235:genetics / Q000502:physiology*; D002454:Cell Differentiation / Q000235:genetics*; D049109:Cell Proliferation; D016000:Cluster Analysis; D005091:Exons / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics; D046228:Microarray Analysis; D008954:Models, Biological; D055495:Neurogenesis / Q000235:genetics / Q000502:physiology; D009474:Neurons / Q000378:metabolism* / Q000502:physiology*; D014407:Tumor Cells, Cultured