Biology subjects

Grabbe, F.

Publications and source records attributed to Grabbe, F..

3 recordsLinked to original sources

bioRxiv2026

The +1 nucleosome functions in Pol II transcription initiation and the transition to elongation

Transcription initiation by RNA polymerase II (Pol II) occurs next to a +1 nucleosome that is positioned downstream of the transcription start site (TSS). The +1 nucleosome has been shown to influence the pre-initiation complex (PIC) assembly and Pol II pausing, but it is unclear whether and how it functions in transcription initiation and the transition to elongation. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome, and we present cryo-EM structures of five intermediate states. First, after PIC assembly, the +1 nucleosome evicts TFIID from the PIC upon binding of ATP to TFIIH. Second, after DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts as a passive border for PIC assembly and a passive barrier for Pol II pausing, but rather has active functions during the initiation-elongation transition of transcription.

molecular biology↗

bioRxiv2025

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

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.

biochemistry↗

bioRxiv2023

Three-step mechanism of promoter escape by RNA polymerase II

The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase (Pol) II and initiation factors are broken to enable promoter escape. Here we reconstitute Pol II promoter escape in vitro, determine high-resolution structures of five transition intermediates, and show that promoter escape occurs in three major steps. First, the growing RNA transcript displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, rewinding of the upstream edge of the growing DNA bubble evicts TFIIA, TFIIB and TBP and repositions parts of TFIIE and TFIIF. Third, binding of DSIF and NELF evicts TFIIE and TFIIH, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of Pol II transcription.

biochemistry↗