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Series GSE106313 Query DataSets for GSE106313
Status Public on Mar 06, 2018
Title Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window in elongation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Spt5 is a highly conserved RNA polymerase II (Pol II)-associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in the absence of Spt5, a fraction of Pol II molecules are dislodged during elongation thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15-20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed and processivity. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning towards maximum elongation speed 15-20 kb from the promoter.
Overall design For all experiments, we ablated the Supt5h gene in vitro by adding 4-hydroxy tamoxifen (4-HT) to primary Supt5hFl/- Rosa26ERT2-cre/+ mouse embryonic fibroblast (MEF) cultures for 72 hours. As controls, we used Rosa26ERT2-cre/+ primary MEFs treated with 4-HT for 72 hours (referred to as wild-type, WT).
Contributor(s) Fitz J, Neumann T, Pavri R
Citation(s) 29514850
Submission date Oct 30, 2017
Last update date May 15, 2019
Contact name Tobias Neumann
Organization name IMP
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (20)
GSM2835825 MEF_4H8_WT_rep2_40942
GSM2835826 MEF_4H8_KO_rep1_20446
GSM2835827 MEF_4H8_KO_rep2_40946
BioProject PRJNA416271
SRA SRP122906

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE106313_GEO_RNASeq_values.txt.gz 637.4 Kb (ftp)(http) TXT
GSE106313_RAW.tar 5.4 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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