title: Detection and measurement of alternative splicing using splicing-sensitive microarrays.
abstract: Splicing and alternative splicing are major processes in the interpretation and expression of genetic information for metazoan organisms. The study of splicing is moving from focused attention on the regulatory mechanisms of a selected set of paradigmatic alternative splicing events to questions of global integration of splicing regulation with genome and cell function. For this reason, parallel methods for detecting and measuring alternative splicing are necessary. We have adapted the splicing-sensitive oligonucleotide microarrays used to estimate splicing efficiency in yeast to the study of alternative splicing in vertebrate cells and tissues. We use gene models incorporating knowledge about splicing to design oligonucleotides specific for discriminating alternatively spliced mRNAs from each other. Here we present the main strategies for design, application, and analysis of spotted oligonucleotide arrays for detection and measurement of alternative splicing. We demonstrate these strategies using a two-intron yeast gene that has been altered to produce different amounts of alternatively spliced RNAs, as well as by profiling alternative splicing in NCI 60 cancer cell lines.
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Karpagam
authors.initials: K
authors.lastname: Srinivasan
authors.forename: Lily
authors.initials: L
authors.lastname: Shiue
authors.forename: Justin D
authors.initials: JD
authors.lastname: Hayes
authors.forename: Ross
authors.initials: R
authors.lastname: Centers
authors.forename: Sean
authors.initials: S
authors.lastname: Fitzwater
authors.forename: Rebecca
authors.initials: R
authors.lastname: Loewen
authors.forename: Lillian R
authors.initials: LR
authors.lastname: Edmondson
authors.forename: Jessica
authors.initials: J
authors.lastname: Bryant
authors.forename: Michael
authors.initials: M
authors.lastname: Smith
authors.forename: Claire
authors.initials: C
authors.lastname: Rommelfanger
authors.forename: Valerie
authors.initials: V
authors.lastname: Welch
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Charles W
authors.initials: CW
authors.lastname: Sugnet
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Howe
authors.forename: Yael
authors.initials: Y
authors.lastname: Mandel-Gutfreund
authors.forename: Manuel
authors.initials: M
authors.lastname: Ares
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D034285:Dynamin II / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008954:Models, Biological; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D022821:RNA Splice Sites; D012680:Sensitivity and Specificity; D012689:Sequence Homology, Nucleic Acid
chemical_list: D022821:RNA Splice Sites; D034285:Dynamin II