Unit:
Κατεύθυνση Κλινική Βιοχημεία - Μοριακή ΔιαγνωστικήLibrary of the School of Science
Supervisors info:
Ανδρέας Σκορίλας, Καθηγητής Κλινικής Βιοχημείας, Τμήμα Βιολογίας, Ε.Κ.Π.Α.
Δημήτριος Γουργιώτης, Καθηγητής Κλινικής Βιοχημείας, Τμήμα Ιατρικής, Ε.Κ.Π.Α.
Διαμάντης Σίδερης, Αναπληρωτής Καθηγητής Βιοχημείας Ευκαρυωτικών Οργανισμών, Τμήμα Βιολογίας, Ε.Κ.Π.Α.
Original Title:
Ταυτοποίηση, ανάλυση και κλινική αξιολόγηση εναλλακτικών μεταγράφων γονιδίων καθώς και μη κωδικών μορίων RNAs (ncRNAs), στο γενετικό τόπο 19q13.3-13.4, με χρήση δεδομένων αλληλούχησης νέας γενιάς, σε καρκινικά κύτταρα
Translated title:
Discovery and expression analysis of novel transcripts and non-coding RNAs (ncRNAs) on chromosome 19q13.3-13.4 in human cancer cells using
Summary:
The human SR-related CTD associated factor 1 (SCAF1) gene is a new member of the human SR (Ser/Arg-rich) superfamily of pre-mRNA splicing factors, which has been discovered and cloned by members of our group. SCAF1 interacts with the CTD domain of the RNA polymerase II and is firmly involved in pre-mRNA splicing. Although it was found to be expressed widely in multiple human tissues, its mRNA levels vary a lot.
The significant relation of SCAF1 with cancer has been confirmed by many studies, since SCAF1 mRNA transcript was found to be overexpressed in breast and ovarian tumors, confirming its significant prognostic value as a cancer biomarker in both these human malignancies.
In this study, we describe the discovery and molecular cloning of fifteen novel transcripts of the human SCAF1 gene (SCAF1 v.2 - v.16), using nested PCR and NGS technology. In detail, extensive bioinformatic analysis revealed that these novel SCAF1 splice variants comprise a total of nine novel alternative splicing events between the annotated exons of the gene, thus producing seven novel SCAF1 transcripts with open-reading frames, which are predicted to encode novel SCAF1 isoforms and eight novel SCAF1 transcripts with premature termination codons that are likely long non-coding RNAs. Additionally, a novel 3' UTR was discovered using 3' RACE and was validated with Sanger sequencing. In order to validate the NGS findings as well as to investigate the expression profile of each novel transcript, RT-PCR experiments were carried out with the use of variant-specific primers.
In conclusion, since SCAF1 is implicated in many human malignancies, qualifying as a potential biomarker, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.
Main subject category:
Science
Keywords:
sequencing, NGS, SCAF1
Number of references:
252
