Inference on paths of yeast transcription pre-initiation complex assembly by model-based analysis of altered occupancy profiles

Transcription dysfunctions lead to serious human diseases. At the molecular level, eukaryotic RNA polymerase II (Pol II) initiates transcription by constructing a pre-initiation complex (PIC) that includes general transcription factors (GTFs), Pol II, and the essential multiprotein coactivator Mediator. Although in vitro experiments suggest a straightforward PIC assembly process, the actual assembly paths in living cells and the role of Mediator in these pathways remain unclear.

One approach involves analyzing changes in the ChIP-seq occupancy profiles of Mediator mutants; however, the interpretation of these data still needs a formal framework. This study aims to address this gap by establishing a quantitative method to rank assembly paths based on their ability to explain the observed ChIP-seq alterations.

The method combines a model of PIC assembly derived from differential equations with parameter optimization that employs a penalized criterion. The researchers tested this framework on data from two yeast Mediator mutants: Med17 and Med10 subunits. The findings reveal that the PIC assembly pathways inferred from in vivo experiments differ from those deduced in a lab setting.

More specifically, the study highlights the importance of distinguishing the core TFIIH module from the TFIIK kinase module in PIC assembly. Additionally, the analysis shows that pathways beginning with Mediator or TBP receive varying levels of support. Interestingly, while several paths fit the data equally well, they differ significantly for particular gene groups.

In conclusion, the study demonstrates that the assembly path can depend on the specific gene and that more than one path may be functional for a single gene in vivo. This research enhances our comprehension of PIC assembly pathways and transcription initiation, paving the way for future modeling and experimental investigations.