title: Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
abstract: Human RCAN3 (regulator of calcineurin 3) belongs to the human RCAN gene family.In this study we provide, with in silico and in vitro analyses, the first detailed description of the human multi-transcript RCAN3 locus. Its analysis revealed that it is composed of a multigene system that includes at least 21 RCAN3 alternative spliced isoforms (16 of them identified here for the first time) and a new RCAN3 antisense gene (RCAN3AS). In particular, we cloned RCAN3-1,3,4,5 (lacking exon 2), RCAN3-1a,2,3,4,5, RCAN3-1a,3,4,5, RCAN3-1b,2,3,4,5, RCAN3-1c,2,3,4,5, RCAN3-1c,2,4,5 and RCAN3-1c,3,4,5, isoforms that present a different 5' untranslated region when compared to RCAN3. Moreover, in order to verify the possible 5' incompleteness of previously identified cDNA isoforms with the reference exon 1, ten more alternative isoforms were retrieved. Bioinformatic searches allowed us to identify RCAN3AS, which overlaps in part with exon 1a, on the opposite strand, for which four different RCAN3AS isoforms were cloned.In order to analyze the different expression patterns of RCAN3 alternative first exons and of RCAN3AS mRNA isoforms, RT-PCR was performed in 17 human tissues. Finally, analyses of RCAN3 and RCAN3AS genomic sequences were performed to identify possible promoter regions, to examine donor and acceptor splice sequences and to compare evolutionary conservation, in particular of alternative exon 1 or 1c--exon 2 junctions in different species.The description of its number of transcripts, of their expression patterns and of their regulatory regions can be important to clarify the functions of RCAN3 gene in different pathways and cellular processes.
authors.affiliation: Center for Research in Molecular Genetics (Fondazione CARISBO), Department of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy. federica.facchin2@unibo.it
authors.forename: Federica
authors.initials: F
authors.lastname: Facchin
authors.forename: Lorenza
authors.initials: L
authors.lastname: Vitale
authors.forename: Eva
authors.initials: E
authors.lastname: Bianconi
authors.forename: Francesco
authors.initials: F
authors.lastname: Piva
authors.forename: Flavia
authors.initials: F
authors.lastname: Frabetti
authors.forename: Pierluigi
authors.initials: P
authors.lastname: Strippoli
authors.forename: Raffaella
authors.initials: R
authors.lastname: Casadei
authors.forename: Maria Chiara
authors.initials: MC
authors.lastname: Pelleri
authors.forename: Allison
authors.initials: A
authors.lastname: Piovesan
authors.forename: Silvia
authors.initials: S
authors.lastname: Canaider
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D001483:Base Sequence; D018899:CpG Islands / Q000235:genetics; D005091:Exons / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D020033:Protein Isoforms / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D020033:Protein Isoforms; C408372:RCAN3 protein, human