|
| Status |
Public on Dec 20, 2021 |
| Title |
The Spt6-tSH2 domain coordinates functional transitions of the RNA Polymerase II CTD during initiation and elongation. |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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 in Rpb1 in a region between the catalytic core and the heptad repeats of its C-terminal domain (CTD). This interaction contributes to the global occupancy of Spt6 within transcription units, suggesting that it has a general role in tethering Spt6 to the elongation complex. However, we show here that disrupting this binding caused increases in some transcripts, revealing specific functional roles in regulating the expression of subsets of genes. These included loci whose regulation involves differential transcription start site selection, early termination of transcription, or efficient restoration of chromatin integrity after transcription. Loss of this interaction also caused a defect in splicing, and apparent pausing of RNAPII progression in regions requiring more complex processing of excised introns. The results support a global role for the Spt6-tSH2:Rpb1 interaction as one of several means of stabilizing the association of Spt6 with RNAPII, but they also reveal local functions at specific sites, especially those where dynamic decisions regarding initiation or termination are made, or where changes in the configuration of associated factors occur. We therefore propose that the Spt6-tSH2:Rpb1 interaction can provide a conduit for communication between RNAPII and the elongation factor function of Spt6, or with other factors associated with the Rpb1 CTD, supporting appropriate elongation through challenging templates and efficient co-transcriptional processing.
|
| |
|
| Overall design |
21 samples (3 replicates each of 7 yeast strains) were grown to logarithmic phase in rich medium at 30C. Cells were collected by centrifugation, RNA was extracted, and RNA-seq was performed.
|
| |
|
| Contributor(s) |
Connell Z, McCullough LL, Parnell TJ, Formosa T |
| Citation(s) |
34967414 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM064649 |
Biochemical, Genetic, and Genomic Analysis of Nucleosome Reorganization by FACT |
UNIVERSITY OF UTAH |
Timothy G Formosa |
| R01 GM116560 |
Structure, mechanism, and function of the histone chaperones Spt6 and FACT |
UNIVERSITY OF UTAH |
Timothy G Formosa |
|
| Submission date |
May 13, 2021 |
| Last update date |
Feb 02, 2022 |
| Contact name |
Tim Formosa |
| E-mail(s) |
TIM@biochem.utah.edu
|
| Phone |
8015815435
|
| Organization name |
University of Utah School of Medicine
|
| Department |
Biochemistry
|
| Street address |
15 N Medical Dr East RM 4100
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112-5650 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL27812 |
Illumina NovaSeq 6000 (Saccharomyces cerevisiae) |
|
| Samples (21)
|
|
| This SubSeries is part of SuperSeries: |
|
| Relations |
| BioProject |
PRJNA729794 |
| SRA |
SRP319772 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE174427_Data_Tables-Each_Gene.xlsx |
8.1 Mb |
(ftp)(http) |
XLSX |
| GSE174427_WT.rpm_f.bw |
22.4 Mb |
(ftp)(http) |
BW |
| GSE174427_WT.rpm_r.bw |
22.2 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-FSP.rpm_f.bw |
23.0 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-FSP.rpm_r.bw |
22.7 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-TPY-FSP.rpm_f.bw |
27.8 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-TPY-FSP.rpm_r.bw |
27.5 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-TPY.rpm_f.bw |
23.1 Mb |
(ftp)(http) |
BW |
| GSE174427_rpb1-TPY.rpm_r.bw |
22.8 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-KK.rpm_f.bw |
26.2 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-KK.rpm_r.bw |
25.9 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-R-KK.rpm_f.bw |
25.8 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-R-KK.rpm_r.bw |
25.5 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-R.rpm_f.bw |
24.1 Mb |
(ftp)(http) |
BW |
| GSE174427_spt6-R.rpm_r.bw |
23.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...