Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.

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 le...

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Autores principales:	Federica Facchin, Lorenza Vitale, Eva Bianconi, Francesco Piva, Flavia Frabetti, Pierluigi Strippoli, Raffaella Casadei, Maria Chiara Pelleri, Allison Piovesan, Silvia Canaider
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d6f8a0e88f5d4b60bd3ad38d9699a4af
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spelling	oai:doaj.org-article:d6f8a0e88f5d4b60bd3ad38d9699a4af2021-11-04T06:08:05ZComplexity of bidirectional transcription and alternative splicing at human RCAN3 locus.1932-620310.1371/journal.pone.0024508https://doaj.org/article/d6f8a0e88f5d4b60bd3ad38d9699a4af2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21961037/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Human 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.Federica FacchinLorenza VitaleEva BianconiFrancesco PivaFlavia FrabettiPierluigi StrippoliRaffaella CasadeiMaria Chiara PelleriAllison PiovesanSilvia CanaiderPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e24508 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Federica Facchin Lorenza Vitale Eva Bianconi Francesco Piva Flavia Frabetti Pierluigi Strippoli Raffaella Casadei Maria Chiara Pelleri Allison Piovesan Silvia Canaider Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
description	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.
format	article
author	Federica Facchin Lorenza Vitale Eva Bianconi Francesco Piva Flavia Frabetti Pierluigi Strippoli Raffaella Casadei Maria Chiara Pelleri Allison Piovesan Silvia Canaider
author_facet	Federica Facchin Lorenza Vitale Eva Bianconi Francesco Piva Flavia Frabetti Pierluigi Strippoli Raffaella Casadei Maria Chiara Pelleri Allison Piovesan Silvia Canaider
author_sort	Federica Facchin
title	Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
title_short	Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
title_full	Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
title_fullStr	Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
title_full_unstemmed	Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.
title_sort	complexity of bidirectional transcription and alternative splicing at human rcan3 locus.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/d6f8a0e88f5d4b60bd3ad38d9699a4af
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Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.

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