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| Status |
Public on Apr 17, 2017 |
| Title |
Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-nexus spike-in] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
RNA polymerase II (Pol II) pauses downstream of the transcription initiation site before beginning productive elongation. This pause is a key component of metazoan gene expression regulation. Some promoters have a strong disposition for Pol II pausing and often mediate faster, more synchronous changes in expression. This requires multiple rounds of transcription and thus cannot rely solely on pause release. But it is unclear how pausing affects the initiation of new transcripts during consecutive rounds of transcription. Using our recently developed ChIP-nexus method, we find that Pol II pausing inhibits new initiation. We propose that paused Pol II helps prevent new initiation between transcription bursts, which may reduce noise.
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| |
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| Overall design |
ChIP-nexus was performed against Pol II in Drosophila melanogaster Kc167 cells. A fix amount of spike-in is added into each sample in order to control for the loss of Pol II ChIP signal after Triptolide treatment or NELF depletion.
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| |
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| Contributor(s) |
Shao W, Zeitlinger J |
| Citation(s) |
28504701 |
| |
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
|
| 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 |
| |
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| Platforms (2) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (14)
|
| GSM2283380 |
Pol II ChIP-nexus with spikein (Control condtion) Rep1 |
| GSM2283381 |
Pol II ChIP-nexus with spikein (Control condtion) Rep2 |
| GSM2283382 |
Pol II ChIP-nexus with spikein (5 min Triptolide treatment) Rep1 |
| GSM2283383 |
Pol II ChIP-nexus with spikein (5 min Triptolide treatment) Rep2 |
| GSM2283384 |
Pol II ChIP-nexus with spikein (10 min Triptolide treatment) Rep1 |
| GSM2283385 |
Pol II ChIP-nexus with spikein (10 min Triptolide treatment) Rep2 |
| GSM2283386 |
Pol II ChIP-nexus with spikein (20 min Triptolide treatment) Rep1 |
| GSM2283387 |
Pol II ChIP-nexus with spikein (20 min Triptolide treatment) Rep2 |
| GSM2283388 |
Pol II ChIP-nexus with spikein (30 min Triptolide treatment) Rep1 |
| GSM2283389 |
Pol II ChIP-nexus with spikein (30 min Triptolide treatment) Rep2 |
| GSM2526133 |
Pol II ChIP-nexus with spikein(Control condtion) Rep1 |
| GSM2526134 |
Pol II ChIP-nexus with spikein(Control condtion) Rep2 |
| GSM2526135 |
Pol II ChIP-nexus with spikein ( (NELF-E and NELF-B knockdown) Rep1 |
| GSM2526136 |
Pol II ChIP-nexus with spikein (NELF-E and NELF-B knockdown) Rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE85741 |
Paused RNA polymerase II inhibits new transcriptional initiation |
|
| Relations |
| BioProject |
PRJNA339232 |
| SRA |
SRP082364 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85739_kc167_dmso_control_polii_chipnexus_spikein_normalized_1_negative.bw |
33.7 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_dmso_control_polii_chipnexus_spikein_normalized_1_positive.bw |
33.7 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_dmso_control_polii_chipnexus_spikein_normalized_2_negative.bw |
42.9 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_dmso_control_polii_chipnexus_spikein_normalized_2_positive.bw |
42.8 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_egfp_rnai_polii_chipnexus_spikein_normalized_and_merged_negative.bw |
75.4 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_egfp_rnai_polii_chipnexus_spikein_normalized_and_merged_positive.bw |
75.2 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_nelfe_b_rnai_polii_chipnexus_spikein_normalized_and_merged_negative.bw |
72.4 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_nelfe_b_rnai_polii_chipnexus_spikein_normalized_and_merged_positive.bw |
72.2 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_10min_polii_chipnexus_spikein_normalized_1_negative.bw |
31.5 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_10min_polii_chipnexus_spikein_normalized_1_positive.bw |
31.4 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_10min_polii_chipnexus_spikein_normalized_2_negative.bw |
19.9 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_10min_polii_chipnexus_spikein_normalized_2_positive.bw |
19.9 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_20min_polii_chipnexus_spikein_normalized_1_negative.bw |
24.2 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_20min_polii_chipnexus_spikein_normalized_1_positive.bw |
24.2 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_20min_polii_chipnexus_spikein_normalized_2_negative.bw |
19.8 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_20min_polii_chipnexus_spikein_normalized_2_positive.bw |
19.8 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_30min_polii_chipnexus_spikein_normalized_1_negative.bw |
45.7 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_30min_polii_chipnexus_spikein_normalized_1_positive.bw |
45.6 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_30min_polii_chipnexus_spikein_normalized_2_negative.bw |
25.6 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_30min_polii_chipnexus_spikein_normalized_2_positive.bw |
25.6 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_5min_polii_chipnexus_spikein_normalized_1_negative.bw |
29.5 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_5min_polii_chipnexus_spikein_normalized_1_positive.bw |
29.5 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_5min_polii_chipnexus_spikein_normalized_2_negative.bw |
24.7 Mb |
(ftp)(http) |
BW |
| GSE85739_kc167_triptolide_5min_polii_chipnexus_spikein_normalized_2_positive.bw |
24.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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