Document Type : Original Article
Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
Department of Biomolecular Sciences, University of Urbino, Via Saffi Urbino, Italy
Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
Department of Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
Objective: The human large intergenic non-coding RNA-regulator of reprogramming program (linc-ROR) is known as a
stem cell specific linc-RNA. linc-ROR counteracts differentiation via sequestering microRNA-145 (miR-145) that targets OCT4 transcript. Despite the research on the expression and function, the exact structure of Linc-ROR transcripts is not clear. Considering the contribution of alternative splicing in transcripts structures and function, identifying different spliced variants of linc-ROR is necessary for further functional analyses. We aimed to find the alternatively spliced transcripts of linc-ROR and investigate their expression pattern in stem and cancer cell lines and during neural differentiation of NT2 cells as a model for understanding linc-ROR role in stem cell and differentiation.
Materials and Methods: In this experimental study, linc-ROR locus was scanned for identifying novel exons. Different primer sets were used to detect new spliced variants by reverse transcription polymerase chain reaction (RT-PCR) and direct sequencing. Quantitative PCR (qPCR) and RT-PCR were employed to profile expression of linc-ROR transcripts in different cell lines and during neural differentiation of stem cells.
Results: We could discover 13 novel spliced variants of linc-ROR harboring unique array of exons. Our work uncovered
six novel exons, some of which were the product of exonized transposable elements. Monitoring expression profile of the linc-ROR spliced variants in a panel of pluripotent and non-pluripotent cells exhibited that all transcripts were primarily expressed in pluripotent cells. Moreover, the examined linc-ROR spliced variants showed a similar downregulation during neural differentiation of NT2 cells.
Conclusion: Altogether, our data showed despite the difference in the structure and composition of exons, various spliced variants of linc-ROR showed similar expression pattern in stem cells and through differentiation.