Fig. 1: Structural analysis of Pol II bound to Alu RNA.
From: Mechanism of mammalian transcriptional repression by noncoding RNA
a, Schematic showing the secondary structure and domain organization of Alu RNA. Alu-LA (orange shading), Alu-RA (purple shading), Alu-RA minimal region (gray shading) and Alu-RA loose region (gray outline) are indicated. The 5′ and 3′ regions of Alu-LA and Alu-RA are indicated with orange and purple bars. Guanosine, green; cytidine, cyan; adenosine, blue; uridine, orange. b, Top-front view of Pol II–Alu-LA and -Alu-RA reconstructions (not B-factor sharpened), with 8-Å-filtered Alu-LA (orange) and Alu-RA (purple) difference densities overlaid. Pol II is colored by subunit. c, Side view of 8-Å-filtered Alu-LA and Alu-RA densities compared to the path of nucleic acids in a transcription EC (PDB ID 5OIK)27. d–h, Structure of Pol II–minimal Alu-RA. d, Top-front view of the locally filtered Pol II–minimal Alu-RA alternative conformation density. e, A rotated view of the modeled region of minimal Alu-RA overlaid with the electron microscopy density (DeepEMhancer postprocessed for visualization). f, Top-front view of the Pol II–minimal Alu-RA structure. g, A view of the DNA–RNA hybrid-like region of minimal Alu-RA and the same region of a transcription EC (PDB ID 5OIK)27. h, As in g, but focused on the downstream DNA region.
