title: In silico investigation of the impact of synonymous variants in ABCB4 gene on mRNA stability/structure, splicing accuracy and codon usage: Potential contribution to PFIC3 disease.
abstract: Progressive Familial Intrahepatic Cholestasis type 3 (PFIC3) is an autosomal-recessive liver disease due to mutations in the ABCB4 gene encoding for the MDR3 protein. In the present study, we performed molecular and bioinformatic analyses in PFIC3 patients in order to understand the molecular basis of the disease. The three studied patients with PFIC3 were screened by PCR amplification followed by direct sequencing of the 27 coding exons of ABCB4. In silico analysis was performed by bioinformatic programs. We revealed three synonymous polymorphisms c.175C>T, c.504C>T, c.711A>T respectively in exon 4, 6, 8 and an intronic c.3487-16T>C variation in intron 26. The computational study of these polymorphic variants using Human Splicing Finder, ex-skip, Mfold and kineFold tools showed the putative impact on the composition of the cis-acting regulatory elements of splicing as well as on the mRNA structure and stability. Moreover, the protein level was affected by codon usage changes estimated by the calculation of ΔRSCU and ΔLog Ratio of codon frequencies interfering as consequence with the accurate folding of the MDR3 protein. As the first initiative of the mutational study of ABCB4 genes in Tunisia, our results are suggestive of a potential downstream molecular effect for the described polymorphisms on the expression pattern of the ABCB4 underlining the importance of synonymous variants.
authors: Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Tunisia. Electronic address: Boudour.khabou.bio@gmail.com.
authors: Boudour
authors: B
authors: Khabou
authors: Department of Life Science, Faculty of Science of Sfax, University of Sfax., Tunisia.
authors: Olfa
authors: O
authors: Siala-Sahnoun
authors: Service of Pediatric, C.H.U. Hedi Chaker Sfax, Tunisia.
authors: Lamia
authors: L
authors: Gargouri
authors: Department of Life Science, Faculty of Science of Sfax, University of Sfax., Tunisia. Electronic address: emna.mkaouar@gmail.com.
authors: Emna
authors: E
authors: Mkaouar-Rebai
authors: Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Tunisia.
authors: Leila
authors: L
authors: Keskes
authors: Service of Pediatric, C.H.U. Hedi Chaker Sfax, Tunisia.
authors: Mongia
authors: M
authors: Hachicha
authors: Department of Life Science, Faculty of Science of Sfax, University of Sfax., Tunisia.
authors: Faiza
authors: F
authors: Fakhfakh
mesh_terms: D018435:ATP Binding Cassette Transporter, Subfamily B / Q000235:genetics*; D002675:Child, Preschool; D002780:Cholestasis, Intrahepatic / Q000235:genetics*; D003062:Codon; D003198:Computer Simulation; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D012326:RNA Splicing; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*
chemical_list: D018435:ATP Binding Cassette Transporter, Subfamily B; D003062:Codon; D012333:RNA, Messenger; C095122:multidrug resistance protein 3
keywords: ABCB4 gene; Codon usage; PFIC3; Splicing; mRNA stability