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Series GSE116244 Query DataSets for GSE116244
Status Public on Apr 05, 2019
Title Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing
Organisms Drosophila melanogaster; Drosophila pseudoobscura
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.
 
Overall design ChIP-seq, ChIP-nexus or 5' RNA-seq was performed using transfected Drosophila Kc167 cells or Drosphila pseudoobscura ML83-63 cell line. Triptolide (TRI) treatment was used to assay the stability of paused Pol II.
 
Contributor(s) Shao W, Garcia-Moreno Alcantara S, Zeitlinger J
Citation(s) 31021316
Submission date Jun 25, 2018
Last update date May 02, 2019
Contact name Julia Zeitlinger
E-mail(s) jbz@stowers.org
Organization name Stowers Institute for Medical Research
Lab Zeitlinger lab
Street address 1000 E 50th Street
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
 
Platforms (2)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
GPL23885 Illumina NextSeq 500 (Drosophila pseudoobscura)
Samples (144)
GSM3215461 reporter_dps_act5c_rpb3_chipnexus
GSM3215462 reporter_dps_pino_rpb3_chipnexus
GSM3215463 reporter_dps_pepck_rpb3_chipnexus
Relations
BioProject PRJNA477850
SRA SRP151305

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Supplementary file Size Download File type/resource
GSE116244_RAW.tar 6.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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