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Series GSE182792 Query DataSets for GSE182792
Status Public on Aug 28, 2021
Title Ssl2/TFIIH Function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary The initial step of RNA polymerase II (Pol II) transcription involves a large number of transcription factors and arises at multiple sites within most promoters. TFIIH is an essential, multi-subunit transcription factor that assembles on promoter DNA with Pol II and five other general transcription factors (GTFs) to form a pre-initiation complex (PIC) for basal transcription. During transcription initiation, TFIIH melts promoter DNA through the ATPase activity of its Ssl2 subunit. In the model eukaryote Saccharomyces cerevisiae, after DNA melting, Pol II scans downstream for usable transcription start sites (TSSs). To understand the function of Ssl2/TFIIH in promoter scanning and TSS selection, we identified novel alleles of SSL2 in genetic screens for mutants defective in TSS distribution that may potentially arise from altered scanning. Consistent with this notion, these ssl2 alleles alter scanning in ways that are distinct from how changes to the Pol II active site alter scanning and this difference is observed genome-wide. Our investigations support two major pathways in controlling promoter scanning and TSS selection, one controlling the efficiency of initiation through Pol II activity or factors regulating Pol II activity; another network appears to control the processivity of scanning by Ssl2/TFIIH.
 
Overall design We report the application of transcription start site sequencing (TSS-seq) and ChIP-exo in high-throughput profiling of RNA polymerase II (Pol II) transcription start site usage and PIC component positioning in the budding yeast Saccharomyces cerevisiae. We applied TSS-seq on six ssl2/TFIIH mutants that were either previously reported defective in Pol II transcription or from our genetic screening indicating possible TSS usage defects. We also applied TSS-seq on wild-type yeast strains and two Pol II mutant that were previously characterized by us for comparison purposes. ChIP-exo was applied on two ssl2/TFIIH mutant that alter TSS usage in distinct patterns to investigate ssl2/TFIIH’s effects on PIC positioning. Raw data of TSS-seq and ChIP-exo were also deposited in NCBI BioProject, under the accession number PRJNA681384.

The GSM records describe a single biological Sample. Submitter created a bioSample (SAMN) for each R1 and R2 read of that single sample.
 
Contributor(s) Zhao T, Lai WK, Kaplan CD
Citation(s) 34652274
BioProject PRJNA681384
Submission date Aug 25, 2021
Last update date Nov 30, 2021
Contact name Tingting Zhao
E-mail(s) tingtingzhao@pitt.edu
Phone 9799859285
Organization name University of Pittsburgh
Street address 4200 Fifth Ave
City Pittsburgh
State/province PA
ZIP/Postal code 15260
Country USA
 
Platforms (1)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (58)
GSM5537055 VV1419_SSL2_WT_TSS-seq_bioreplicate_1
GSM5537056 VV1420_SSL2_WT_TSS-seq_bioreplicate_2
GSM5537057 VV1421_SSL2_WT_TSS-seq_bioreplicate_2
Relations
SRA SRP295731

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE182792_RAW.tar 263.8 Mb (http)(custom) TAR (of BEDGRAPH, CSV, TXT)
GSE182792_processed_data.tar.gz 135.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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