Structural basis of a transcription pre-initiation complex on a divergent promoter

• Published in: Molecular cell 2023-02, Vol.83 (4), p.574-588.e11
• Main Authors: Gorbea Colón, Jose J., Palao, Leon, Chen, Shin-Fu, Kim, Hee Jong, Snyder, Laura, Chang, Yi-Wei, Tsai, Kuang-Lei, Murakami, Kenji
• Format: Article
• Language: English
• Subjects: activator; cross-linking mass spectrometry; cryo-EM; cryo-ET; Cryoelectron Microscopy; divergent transcription; enhancer; Mediator; Mediator Complex - genetics; promoter commitment; Promoter Regions, Genetic; promoter-enhancer looping; RNA Polymerase II - metabolism; RNA polymerase II pre-initiation complex; Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism; Transcription Initiation, Genetic; Transcription, Genetic; UAS
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2023.01.011

Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription. [Display omitted] •Structure of two distinct Med-PICs on a divergent promoter•Two distinct Med-PICs are recruited by a homodimeric activator protein•Core promoter commitment is facilitated by late GTFs•Dynamic changes in DNA organization during transcription initiation Gorbea et al. solved the cryo-EM structure of a yeast Mediator-pre-initiation complex assembled on a divergent promoter. The complex dimerizes through a homodimeric activator protein and requires late general transcription factors for core promoter commitment. These findings open new avenues to determine the mechanisms of divergent transcription widespread in eukaryotes.