Long non coding RNA (lncRNA) SCIRT regulates mitotic and stemness genes in breast cancer stem cells

CHART sequencing has been carried out in order to evaluate SCIRT target genes in MDA-MB-231 sphere derived cells. We discovered that lncRNA SCIRT binds promoter region of genes whose expression changes after SCIRT siRNA downregulation, suggesting that those are target SCIRT target genes. The genome-wide binding profile of lncRNA SCIRT was determined using Capture Hybridization Analysis of RNA Targets (CHART)-Seq technique (Simon et al, Proc Natl Acad Sci U S A 108: 20497-20502, 2011) in MDA-MB-231 sphere-derived cells. Following the CHART-seq protocol, we used RNase H elution to recover genomic DNA associated with endogenous SCIRT transcripts and genomic DNA associated with a control oligonucleotide (corresponding to the E.coli LacZ sequence). We identified SCIRT binding sites in comparison both to DNA recovered using the control LacZ oligonucleotide and to an input DNA sample from MDA-MB-231 sphere derived cells.