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

Authors :
Giuseppe Viglietto
Alessandro Weisz
Enrico Iaccino
Antonio Pisano
Gaetanina Golino
Marilena Pontoriero
Annarita Scialdone
Sergio Paduano
Francesca Rizzo
Eleonora Vecchio
Simona Ceglia
Selena Mimmi
Giuseppe Scala
Maria R. De Filippo
Giuseppe Fiume
Francesco Albano
Carmelo Laudanna
Ileana Quinto
Camillo Palmieri
Source :
International Journal of Molecular Sciences, Vol 17, Iss 11, p 1848 (2016), International Journal of Molecular Sciences, International Journal of Molecular Sciences; Volume 17; Issue 11; Pages: 1848
Publication Year :
2016
Publisher :
MDPI AG, 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.

Details

Language :
English
ISSN :
14220067
Volume :
17
Issue :
11
Database :
OpenAIRE
Journal :
International Journal of Molecular Sciences
Accession number :
edsair.doi.dedup.....708093a02df473d0b96a7cb00e60941e