|
| Status |
Public on Apr 17, 2017 |
| Title |
Paused RNA polymerase II inhibits new transcriptional initiation [ChIP-nexus] |
| 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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| |
|
| Overall design |
ChIP-nexus was performed against Pol II, TBP, TFIIA, TFIIB, TFIIF, TAF2, XPB and NELF-E in Drosophila melanogaster Kc167 cells.
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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) |
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) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
|
| Samples (41)
|
| GSM2283349 |
TAF2 ChIP-nexus (Control condtion) Rep1 |
| GSM2283350 |
TAF2 ChIP-nexus (Control condtion) Rep2 |
| GSM2283351 |
TBP ChIP-nexus (Control condtion) Rep1 |
| GSM2283352 |
TBP ChIP-nexus (Control condtion) Rep2 |
| GSM2283353 |
TFIIA ChIP-nexus (Control condtion) Rep1 |
| GSM2283354 |
TFIIA ChIP-nexus (Control condtion) Rep2 |
| GSM2283355 |
TFIIB ChIP-nexus (Control condtion) Rep1 |
| GSM2283356 |
TFIIB ChIP-nexus (Control condtion) Rep2 |
| GSM2283357 |
TFIIF ChIP-nexus (Control condtion) Rep1 |
| GSM2283358 |
TFIIF ChIP-nexus (Control condtion) Rep2 |
| GSM2283359 |
XPB ChIP-nexus (Control condtion) Rep1 |
| GSM2283360 |
XPB ChIP-nexus (Control condtion) Rep2 |
| GSM2283361 |
Pol II ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283362 |
Pol II ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283363 |
TAF2 ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283364 |
TAF2 ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283365 |
TBP ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283366 |
TBP ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283367 |
TFIIA ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283368 |
TFIIA ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283369 |
TFIIB ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283370 |
TFIIB ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283371 |
TFIIF ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283372 |
TFIIF ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283373 |
XPB ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2283374 |
XPB ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2283377 |
Pol II ChIP-nexus Rep1 |
| GSM2283378 |
TFIIA ChIP-nexus Rep1 |
| GSM2283379 |
TFIIB ChIP-nexus Rep1 |
| GSM2523055 |
Pol II ChIP-nexus (Control condtion) Rep1 |
| GSM2523056 |
Pol II ChIP-nexus (Control condtion) Rep2 |
| GSM2523057 |
NELF-E ChIP-nexus (Control condtion) Rep1 |
| GSM2523058 |
NELF-E ChIP-nexus (Control condtion) Rep2 |
| GSM2523059 |
NELF-E ChIP-nexus (1 h Triptolide treatment) Rep1 |
| GSM2523060 |
NELF-E ChIP-nexus (1 h Triptolide treatment) Rep2 |
| GSM2523061 |
Pol II ChIP-nexus (1 h 0.5 uM Triptolide treatment) Rep1 |
| GSM2523062 |
Pol II ChIP-nexus (1 h 500 uM Triptolide treatment) Rep1 |
| GSM2523063 |
Pol II ChIP-nexus (1 h 0.5 uM Flavopiridol treatment) Rep1 |
| GSM2523064 |
Pol II ChIP-nexus (1 h 0.5 uM Flavopiridol treatment) Rep2 |
| GSM2523065 |
Pol II ChIP-nexus (1 h 50 uM DRB treatment) Rep1 |
| GSM2523066 |
Pol II ChIP-nexus (1 h 50 uM DRB treatment) Rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE85741 |
Paused RNA polymerase II inhibits new transcriptional initiation |
|
| Relations |
| BioProject |
PRJNA339233 |
| SRA |
SRP082363 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85738_RAW.tar |
252.0 Mb |
(http)(custom) |
TAR (of BW) |
| GSE85738_kc167_dmso_nelfe_chipnexus_normalized_and_merged_negative.bw |
96.8 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_nelfe_chipnexus_normalized_and_merged_positive.bw |
96.8 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_polii_chipnexus_normalized_and_merged_negative.bw |
91.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_polii_chipnexus_normalized_and_merged_positive.bw |
91.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_taf2_chipnexus_normalized_and_merged_negative.bw |
120.4 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_taf2_chipnexus_normalized_and_merged_positive.bw |
120.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tbp_chipnexus_normalized_and_merged_negative.bw |
68.7 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tbp_chipnexus_normalized_and_merged_positive.bw |
68.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiia_chipnexus_normalized_and_merged_negative.bw |
154.0 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiia_chipnexus_normalized_and_merged_positive.bw |
153.9 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiib_chipnexus_normalized_and_merged_negative.bw |
92.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiib_chipnexus_normalized_and_merged_positive.bw |
92.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiif_chipnexus_normalized_and_merged_negative.bw |
43.8 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_tfiif_chipnexus_normalized_and_merged_positive.bw |
43.8 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_xpb_chipnexus_normalized_and_merged_negative.bw |
55.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_dmso_xpb_chipnexus_normalized_and_merged_positive.bw |
55.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_drb_50um_polii_chipnexus_normalized_and_merged_negative.bw |
64.7 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_drb_50um_polii_chipnexus_normalized_and_merged_positive.bw |
64.7 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_flavopiridol_0.5um_polii_chipnexus_normalized_and_merged_negative.bw |
80.9 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_flavopiridol_0.5um_polii_chipnexus_normalized_and_merged_positive.bw |
80.8 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_flavopiridol_polii_chipnexus_normalized_and_merged_negative.bw |
38.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_flavopiridol_polii_chipnexus_normalized_and_merged_positive.bw |
38.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_polii_chipnexus_normalized_negative.bw |
16.0 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_polii_chipnexus_normalized_positive.bw |
15.9 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_tfiia_chipnexus_normalized_negative.bw |
22.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_tfiia_chipnexus_normalized_positive.bw |
22.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_tfiib_chipnexus_normalized_negative.bw |
19.4 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_tfiib_chipnexus_normalized_positive.bw |
19.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_nelfe_chipnexus_normalized_and_merged_negative.bw |
137.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_nelfe_chipnexus_normalized_and_merged_positive.bw |
137.0 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_polii_chipnexus_normalized_and_merged_negative.bw |
58.4 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_polii_chipnexus_normalized_and_merged_positive.bw |
58.3 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_taf2_chipnexus_normalized_and_merged_negative.bw |
77.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_taf2_chipnexus_normalized_and_merged_positive.bw |
77.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tbp_chipnexus_normalized_and_merged_negative.bw |
47.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tbp_chipnexus_normalized_and_merged_positive.bw |
47.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiia_chipnexus_normalized_and_merged_negative.bw |
62.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiia_chipnexus_normalized_and_merged_positive.bw |
62.5 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiib_chipnexus_normalized_and_merged_negative.bw |
75.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiib_chipnexus_normalized_and_merged_positive.bw |
75.1 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiif_chipnexus_normalized_and_merged_negative.bw |
34.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_tfiif_chipnexus_normalized_and_merged_positive.bw |
34.6 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_xpb_chipnexus_normalized_and_merged_negative.bw |
42.2 Mb |
(ftp)(http) |
BW |
| GSE85738_kc167_triptolide_xpb_chipnexus_normalized_and_merged_positive.bw |
42.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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