differential expression pattern of linc-ror spliced variants in pluripotent and non-pluripotent cell lines

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.