Structure and Function of Activated Transcription Elongation through Chromatin

Abstract

The eukaryotic genome is organized into chromatin, whose basic unit consists of around 147 base pairs of DNA wrapped around a histone octamer core. This level of compaction becomes a barrier to processes such as DNA replication or transcription. To overcome this barrier, transcription through chromatin is regulated by several elongation factors, histone chaperones, and chromatin remodelers that help RNA polymerase II (Pol II) progress through nucleosomes while maintaining chromatin structure. This work investigates the role of the highly conserved IWS1 (interacts with SPT6 1), which is a histone chaperone and core elongation factor, but its exact mechanism during transcription is unclear. Using cryo- EM, we identify that a series of short linear motifs (SLiMs) within the disordered IWS1 C-terminus make multiple contacts with the elongation complex. Biochemical assays reveal that the SLiMs are required for transcription stimulation by IWS1 on linear and chromatinized DNA substrates. Further mutational studies demonstrate that the extreme C-terminus of IWS1 is necessary for recruitment of IWS1 to the elongation complex through its interaction with the RPB1 jaw. Due to the crucial role of the RPB1 jaw interaction in IWS1 recruitment, we perform an AlphaFold-Multimer screen that reveals multiple other factors which also bind to the RPB1 jaw. Then, we directly demonstrate that IWS1 protects the elongation complex from transcriptional stalling induced by the helicase RECQL5 in a manner dependent on their RPB1 jaw interactions. This work provides the structure of the most complete activated mammalian transcription elongation complex, elucidates the function of the IWS1 C-terminus in chromatin transcription, and presents a model for how Pol II is regulated through different transcription states.