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Series GSE45873 Query DataSets for GSE45873
Status Public on May 01, 2013
Title Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription.
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary TFIID is a central player in activated transcription initiation. Recent evidence suggests that the role and composition of TFIID is more diverse than previously understood. To investigate the effects of changing the composition of TFIID in a simple system we depleted TAF1 from Drosophila cells and determined the consequences on metal induced transcription at an inducible gene, Metallothionein B (MtnB). We observe a marked increase in the levels of both the mature message and pre-mRNA in TAF1 depleted cells. Under conditions of continued metal exposure, we show that TAF1 depletion increases the magnitude of the initial transcription burst, but has no effect on the timing of that burst. We also show that TAF1 depletion causes delay in the shut-off of transcription upon removal of the stimulus. Thus TAFs are involved in both establishing an upper limit of transcription during induction and efficiently turning the gene off once the inducer is removed. Using genomewide nascent-seq we identify hundreds of genes that are controlled in a similar manner indicating that the findings at this inducible gene are likely generalizable to a large set of promoters. There is a long-standing appreciation for the importance of the spatial and temporal control of transcription. Here we uncover an important third dimension of control, the magnitude of the response. Our results show that the magnitude of the transcriptional response to the same signaling event, even at the same promoter, can vary greatly depending on the composition of the TFIID complex in the cell.
 
Overall design Nascent RNA was sequenced from replicate samples of Drosophila S2 cells treated with double-stranded RNA directed against E. coli LacI (Control) or against Drosophlia TAF1 (experimental). Reads per kilo-base per million (RPKM) was determined for each gene and the control and experimental samples were compared to determine the genes that were affected by the depletion of TAF1.
 
Contributor(s) Marr S, Pennington K, Chirn G, Marr M
Citation(s) 23610421
Submission date Apr 08, 2013
Last update date May 15, 2019
Contact name Michael Marr
E-mail(s) mmarr@brandeis.edu
Organization name Brandeis University
Department Biology
Street address 415 South St
City Waltham
State/province Massachusetts
ZIP/Postal code 02454
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (4)
GSM1117140 050112lac.fastq.gz
GSM1117141 050112taf1.fastq.gz
GSM1117142 nLac.fastq.gz
Relations
BioProject PRJNA196526
SRA SRP020625

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
GSE45873_RAW.tar 1.5 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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