Repression of RNA Polymerase II Transcription by B2 RNA Depends on a Specific Pattern of Structural Regions in the RNA

B2 RNA is a mouse non-coding RNA that binds directly to RNA polymerase II (Pol II) and represses transcription by disrupting critical interactions between the polymerase and promoter DNA. How the structural regions within B2 RNA work together to mediate transcriptional repression is not well understood. To address this question, we systematically deleted structural regions from B2 RNA and determined the effects on transcriptional repression using a highly purified Pol II in vitro transcription system. Deletions that compromised the ability of B2 RNA to function as a transcriptional repressor were also tested for their ability to bind directly to Pol II, which enabled us to distinguish regions uniquely important for repression from those important for binding. We found that transcriptional repression requires a pattern of RNA structural motifs consisting of an extended single-stranded region bordered by two stem‑loops. Hence, there is modularity in the function of the stem-loops in B2 RNA—when one stem‑loop is deleted, another can take its place to enable transcriptional repression.