Structural Biology of RNA Polymerase II Transcription: 20 Years On

Abstract

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 36 is October 6, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Transcription activation is enhanced by multivalent interactions independent of phase separation

“…We find that efficient transcription activation depends not only dependent on TF binding site occupancy but also requires a sufficiently long TF residence time. Thus, reactions between the TF binding step and the start of transcription are likely to involve a kinetic proofreading mechanism, as for example nucleosome remodeling (13) or ATP-dependent promoter DNA melting (3). It is noted that our analysis for the first time directly demonstrates how transcription activation strength is reduced with shorter residence time in an otherwise identical system and while maintaining the same degree of binding site occupancy.…”

“…or ATP-dependent promoter DNA melting(3). It is noted that our analysis for the first time directly demonstrates how transcription activation strength is reduced with shorter residence time in an otherwise identical system and while maintaining the same degree of binding site occupancy.…”

“…Apochromat 20x/0.8 M27), the Zen 2012 pro software including modules for z-stack, timelapse and multi-position acquisition and an AxioCam MRm Rev 3. monochrome camera with filter sets with excitation bandpass, beam splitter, emission bandpass wavelength: GFP, 470/40 nm, 495 nm, 525/50 nm; tdTomato, 535/30 nm, 570 nm, 572/25 nm and mCherry, 550/25 nm, 590 nm, 629/62 nm.…”

How structural biology transformed studies of transcription regulation

“…Since virtually all of these complexes contain proteins whose structures had been determined, usually by x-ray crystallography, the ready availability of coordinates and associated data in the Protein Data Bank has greatly facilitated map interpretation and model building. The many structures of basal transcription factors bound to DNA, such as TBP (1YTB, 1VTL) (44,45), TFIIA (78), and TFIIB (79), and RNA polymerase II have provided the foundation on which to interpret structures of transcription initiation and elongation complexes (for a comprehensive recent review, see (20)). The change in the PDB coordinate data format to mmCIF/PDBx (80) was another advance that facilitated working with such large structures.…”

Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

“…RNA polymerase II (RNAPII) transcribes DNA of eukaryotic genomes into RNA molecules (Osman & Cramer, 2020). Widespread transcriptional activity of RNAPII in non-proteincoding regions of genome results in non-protein-coding RNAs (David et al, 2006;Kapranov et al, 2007;Core et al, 2008).…”