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Int. J. Mol. Sci. 2016, 17(11), 1848; doi:10.3390/ijms17111848

IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells

1
Department of Experimental and Clinical Medicine, University ‘Magna Graecia’ of Catanzaro, Viale Europa (Località Germaneto), 88100 Catanzaro, Italy
2
Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Schola Medica Salernitana’, University of Salerno, via S. Allende 1, 84081 Baronissi, Italy
3
Department of Health Sciences, University “Magna Graecia”, 88100 Catanzaro, Italy
Present address: Department of Hematology and Transfusion Medicine, Medical Faculty, University of Lund, 221 00 Lund, Sweden.
Present address: Center for Translational Genomics and Bioinformatics, Ospedale San Raffaele, 20132 Milano, Italy.
*
Authors to whom correspondence should be addressed.
Academic Editor: William Chi-shing Cho
Received: 22 July 2016 / Revised: 21 October 2016 / Accepted: 31 October 2016 / Published: 7 November 2016
(This article belongs to the Special Issue Next-Generation Sequencing for Clinical Application)
View Full-Text   |   Download PDF [7581 KB, uploaded 7 November 2016]   |  

Abstract

The IBTK gene encodes the major protein isoform IBTKα that was recently characterized as substrate receptor of Cul3-dependent E3 ligase, regulating ubiquitination coupled to proteasomal degradation of Pdcd4, an inhibitor of translation. Due to the presence of Ankyrin-BTB-RCC1 domains that mediate several protein-protein interactions, IBTKα could exert expanded regulatory roles, including interaction with transcription regulators. To verify the effects of IBTKα on gene expression, we analyzed HeLa and K562 cell transcriptomes by RNA-Sequencing before and after IBTK knock-down by shRNA transduction. In HeLa cells, 1285 (2.03%) of 63,128 mapped transcripts were differentially expressed in IBTK-shRNA-transduced cells, as compared to cells treated with control-shRNA, with 587 upregulated (45.7%) and 698 downregulated (54.3%) RNAs. In K562 cells, 1959 (3.1%) of 63128 mapped RNAs were differentially expressed in IBTK-shRNA-transduced cells, including 1053 upregulated (53.7%) and 906 downregulated (46.3%). Only 137 transcripts (0.22%) were commonly deregulated by IBTK silencing in both HeLa and K562 cells, indicating that most IBTKα effects on gene expression are cell type-specific. Based on gene ontology classification, the genes responsive to IBTK are involved in different biological processes, including in particular chromatin and nucleosomal organization, gene expression regulation, and cellular traffic and migration. In addition, IBTK RNA interference affected RNA maturation in both cell lines, as shown by the evidence of alternative 3′- and 5′-splicing, mutually exclusive exons, retained introns, and skipped exons. Altogether, these results indicate that IBTK differently modulates gene expression and RNA splicing in HeLa and K562 cells, demonstrating a novel biological role of this protein. View Full-Text
Keywords: Next Generation Sequencing; IBTK; Cul3-dependent E3 ligase; transcription Next Generation Sequencing; IBTK; Cul3-dependent E3 ligase; transcription
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Fiume, G.; Scialdone, A.; Rizzo, F.; De Filippo, M.R.; Laudanna, C.; Albano, F.; Golino, G.; Vecchio, E.; Pontoriero, M.; Mimmi, S.; Ceglia, S.; Pisano, A.; Iaccino, E.; Palmieri, C.; Paduano, S.; Viglietto, G.; Weisz, A.; Scala, G.; Quinto, I. IBTK Differently Modulates Gene Expression and RNA Splicing in HeLa and K562 Cells. Int. J. Mol. Sci. 2016, 17, 1848.

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