Structure of human cytoplasmic Pol II complex explains global transcription repression by Gdown1

Abstract

RNA polymerase II (Pol II) is a 12-subunit enzyme crucial for gene transcription in the nucleus. However, its assembly in the cytoplasm, nuclear import, and nuclear function of assembly factors remain poorly understood. Here, we isolated Pol II from the cytoplasmic fraction of human cells (cfPol II) and determined its cryo-EM structure. The structure reveals that Pol II is fully assembled in the cytoplasm before nuclear import. We also found that Gdown1 binds Pol II through three distinct regions, indicating it may stabilize Pol II assembly intermediates. Notably, Gdown1 binding precludes the association of essential transcription factors IIB and IIF, rendering cfPol II inactive in promoter-dependent transcription in vitro. Our results provide a basis for Gdown1-dependent global transcription repression and suggest a model for the role of Gdown1 in Pol II assembly, import, and transcription regulation.