 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 26, 2018 |
| Title |
Gcn4 binding in coding regions can activate internal and canonical 5’ promoters in yeast [RNA-seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding. Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ~300 Gcn4-bound sites are within coding sequences (CDS), with ~75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDS, adjacent to induced TBP peaks—consistent with Gcn4 activation of cryptic, bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDS can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters.
|
| |
|
| Overall design |
We analyzed the transcriptome in wild type yeast cells after induction by 3-AT and SM by RNA-seq. The ChIP-seq data is GSE107532.
|
| |
|
| Contributor(s) |
Rawal Y, Chereji RV, Valabhoju V, Qiu H, Ocampo J, Clark DJ, Hinnebusch AG |
| Citation(s) |
29628310 |
| |
| Submission date |
Feb 09, 2018 |
| Last update date |
Mar 13, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
|
| Phone |
301-435-8670
|
| Organization name |
National Institutes of Health
|
| Department |
NICHD
|
| Lab |
David J. Clark Lab
|
| Street address |
6 Center Drive, Room 2A14
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (12)
|
| GSM2991004 |
Untreated, biological replicate 1 (3AT) |
| GSM2991005 |
3AT-treated for 1 min, biological replicate 1 |
| GSM2991006 |
3AT-treated for 5 min, biological replicate 1 |
| GSM2991007 |
3AT-treated for 10 min, biological replicate 1 |
| GSM2991008 |
3AT-treated for 20 min, biological replicate 1 |
| GSM2991009 |
3AT-treated for 40 min, biological replicate 1 |
| GSM2991010 |
Untreated, biological replicate 2 (3AT) |
| GSM2991011 |
3AT-treated for 40 min, biological replicate 2 |
| GSM2991012 |
Untreated, biological replicate 1 (SM) |
| GSM2991013 |
SM-treated for 25 min, biological replicate 1 |
| GSM2991014 |
Untreated, biological replicate 2 (SM) |
| GSM2991015 |
SM-treated for 25 min, biological replicate 2 |
|
| Relations |
| BioProject |
PRJNA433659 |
| SRA |
SRP132584 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110413_RAW.tar |
355.6 Mb |
(http)(custom) |
TAR (of TDF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...