Spt5's central KOW domains and the Pol II Stalk Collaborate to Regulate Chromatin and 3'-End Processing

Spt5 is a universally conserved multidomain transcription elongation factor that acts as a component of all Pol II elongation complexes. Structural studies indicate that several of Spt5s central KOW domains lie adjacent to the Pol II stalk, composed of subunits Rpb4 and Rpb7. However, their in vivo functions are unknown. Here we show that Spt5 and Rpb4/7 jointly modulate 3-end formation and co-transcriptional chromatin integrity in Saccharomyces cerevisiae. We identify mutations in the SPT5 KOW2-3 domains and RPB7 that cause cryptic initiation of transcription and alter 3-end formation of RNA transcripts. Molecular readthrough assays reveal allele-specific changes at both GAL10 and SNR13, consistent with impacts on CPF/CF- and NNS-dependent termination. Proteomic experiments with isolated KOW2-3 domain enrich factors from both pathways as well as chromatin regulators, overlapping known Rpb7 interactors. Together, these findings support a model in which Spt5 KOW2-3/Pol II stalk region acts as a recruitment platform that coordinates pre-mRNA processing and chromatin dynamics during elongation, revealing new roles for the central KOW domains of Spt5. SummaryThis work describes a cooperative in vivo function for Spt5s central KOW domains and the Pol II stalk in Saccharomyces cerevisiae. Allele-specific genetics and reporter assays show cooperative effects of SPT5 and RPB4/7 on cryptic initiation and 3'-end formation; double-mutant analyses reveal synthetic interactions. RT-qPCR at GAL10 and SNR13 demonstrates regulation of both poly(A) and non-coding transcript termination. Spt5 KOW pull-down proteomics enrich poly(A) and non-coding termination factors, as well as chromatin regulators that overlap with known Rpb7 interactors. Together, the data support a model in which Spt5 and the Pol II stalk coordinate chromatin integrity and termination during elongation.