RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells.

Monica Rienzo, Valerio Costa, Margherita Scarpato, Concetta Schiano, Amelia Casamassimi, Vincenzo Grimaldi, Alfredo Ciccodicola, Claudio Napoli

Journal: Gene 2014;547(1):98-105

PMID: 24952135

Full Text on Elsevier Science View on PubMed

Abstract

Mediator (MED) complex is a multiprotein playing a key role in the eukaryotic transcription. Alteration of MED function may have enormous pathophysiological consequences and several MED genes have been implicated in human diseases. Here, we have combined computational and experimental approaches to identify and characterize, new transcripts generated by alternative splicing (AS) for all MED genes, through the analysis of our recently published RNA-Sequencing datasets of endothelial progenitor cells (EPCs). This combined strategy allowed us to identify novel transcripts for MED4, MED9, MED11, MED14, MED27 and CDK8 most of them generated by AS. All the newly identified transcripts, except MED11, are predicted to encode novel protein isoforms. The identification of novel MED variants could lead to the finding of other MED complexes with different functions depending on their subunit composition. Finally, the expression profile of all MED genes, together with an extensive gene expression analysis, may be useful to better classify the diverse subsets of cell populations that contribute to neovascularization.

Address: Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy. Electronic address: [email protected].; Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy.; Institute of Diagnostic and Nuclear Development (SDN), IRCCS, Via E. Gianturco 113, 80143 Naples, Italy.; Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy.; U.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology [SIMT], Regional Reference Laboratory of Transplant Immunology [LIT], Azienda Universitaria Policlinico (AOU), 1st School of Medicine, Second University of Naples, Piazza Miraglia 2, 80138 Naples, Italy.; Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio 7, 80138 Naples, Italy; Institute of Diagnostic and Nuclear Development (SDN), IRCCS, Via E. Gianturco 113, 80143 Naples, Italy; U.O.C. Immunohematology, Transfusion Medicine and Transplant Immunology [SIMT], Regional Reference Laboratory of Transplant Immunology [LIT], Azienda Universitaria Policlinico (AOU), 1st School of Medicine, Second University of Naples, Piazza Miraglia 2, 80138 Naples, Italy.

DOI: 10.1016/j.gene.2014.06.034

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MeSH Terms: Amino Acid Sequence, Binding Sites, Cells, Cultured, Endothelial Cells, Humans, Mediator Complex, MicroRNAs, Molecular Sequence Data, RNA, Messenger, Sequence Analysis, RNA, Sequence Homology, Amino Acid, Stem Cells