The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II

• Published in: Nucleic acids research Vol. 50; no. 2; pp. 784 - 802
• Main Authors: Connell, Zaily, Parnell, Timothy J, McCullough, Laura L, Hill, Christopher P, Formosa, Tim
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 25-01-2022
• Subjects: Binding Sites; Gene Expression Regulation; Gene regulation, Chromatin and Epigenetics; Histone Chaperones - chemistry; Histone Chaperones - genetics; Histone Chaperones - metabolism; Humans; IMP Dehydrogenase - metabolism; Models, Biological; Models, Molecular; Mutation; Protein Binding; Protein Conformation; RNA Polymerase II - chemistry; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; src Homology Domains; Structure-Activity Relationship; Transcription Initiation Site; Transcription, Genetic; Transcriptional Elongation Factors - chemistry; Transcriptional Elongation Factors - genetics; Transcriptional Elongation Factors - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkab1262

Abstract
The conserved transcription elongation factor Spt6 makes several contacts with the RNA Polymerase II (RNAPII) complex, including a high-affinity interaction between the Spt6 tandem SH2 domain (Spt6-tSH2) and phosphorylated residues of the Rpb1 subunit in the linker between the catalytic core and the C-terminal domain (CTD) heptad repeats. This interaction contributes to generic localization of Spt6, but we show here that it also has gene-specific roles. Disrupting the interface affected transcription start site selection at a subset of genes whose expression is regulated by this choice, and this was accompanied by changes in a distinct pattern of Spt6 accumulation at these sites. Splicing efficiency was also diminished, as was apparent progression through introns that encode snoRNAs. Chromatin-mediated repression was impaired, and a distinct role in maintaining +1 nucleosomes was identified, especially at ribosomal protein genes. The Spt6-tSH2:Rpb1 interface therefore has both genome-wide functions and local roles at subsets of genes where dynamic decisions regarding initiation, transcript processing, or termination are made. We propose that the interaction modulates the availability or activity of the core elongation and histone chaperone functions of Spt6, contributing to coordination between RNAPII and its accessory factors as varying local conditions call for dynamic responses.
Graphical Abstract
Graphical Abstract
RNAPII is recruited to a promoter and forms a pre-initiation complex. Conversion of the PIC to an elongation complex involves loading multiple factors that promote elongation, modify chromatin, and process the emerging transcript. Many of these factors are associated with the heptad repeats of the CTD of Rpb1 (gray shapes bound to green line). The Spt6 core domain has conserved functions in RNAPII elongation, and we propose that the Spt6-tSH2 domain coordinates these elongation functions with the activities of the factors associated with the Rpb1 CTD by orienting the CTD and mediating interactions among the factors, the other domains of Spt6, and the catalytic engine of RNAPII.