Promoter-associated RNAs (paRNA) are long noncoding RNAs transcribed in sense or antisense direction in correspondence of promoters of other genes. Their expression influences promoter activity by means of specific regulatory function. PaRNA can act as a scaffold for proteins involved in processes regulating gene expression, as chromatin remodeling or transcription. RNA-induced transcriptional silencing (RITS) is the mechanism of transcriptional interference achieved by siRNA directed against chromatin-associated RNAs, as paRNAs. In this chapter, it is described how to detect interaction between siRNA and paRNA in cell nuclei and investigate siRNA capability to destabilize paRNA-protein complex.
Keywords: RNA immunoprecipitation; biotin pull down; directional RT-PCR; noncoding RNA.