P60. Functional analysis of stem cell-specific long non-coding RNAs in human embryonic carcinoma cell line NCCIT

Abstract

Human stem cells are characterized by the ability for self-renewal and differentiation potential. These characteristics are likely governed by tight regulation of a molecular network that includes POU5F1, SOX2, and NANOG. In addition to known genes, transcriptome profiling studies have also identified a large number of novel transcripts that appear to be significantly expressed in stem cells. Several novel targets previously identified by reverseSAGE were investigated and these transcripts appear to be long non-coding RNAs. Two of these, HEST097 and HEST147, were further studied to determine possible connections to the stem cell fate. Real-time PCR showed specific expression of these targets in human embryonic stem cells (hESCs) and human embryonic carcinomas (hECCs), with little expression in other cell types, and was confirmed by SAGE database analysis. RNAi knockdown of HEST097 and HEST147 in hECC cell line NCCIT produced minor morphological changes and no overt signs of differentiation despite downregulation of NANOG. Cell proliferation appeared to be reduced and cell cycle markers were also affected. Intriguingly, siRNA knockdown of HEST147 resulted in downregulation of FGF4 expression, a gene that is located on the chromosome region downstream to HEST147. This may possibly point towards a role in which the stability of a long non-coding RNA may affect expression of a neighbouring transcript on its chromosome location. The discovery of these stem cell-specific transcripts raises interesting questions where further studies would be required in order to determine the possible mechanisms in which long non-coding RNAs may affect the stem cell fate.