 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 15, 2023 |
| Title |
ISGF3 and STAT2/IRF9 direct basal and IFN-induced transcription through genome-wide binding of phosphorylated and unphosphorylated complexes to commonly ISRE containing ISGs [ChIP-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To further understand the role of phosphorylation in ISGF3- and STAT2/IRF9-mediated constitutive and long-term IFN-I-stimulated transcriptional responses, we performed RNA-Seq and ChIP-Seq, in combination with phosphorylation inhibition and anti-viral experiments. First, we identified a group of ISRE-containing ISGs that were commonly regulated in IFNα treated WT and STAT1-KO cells. Thus, in 2fTGH and Huh7.5 WT cells IFNα-inducible transcription and anti-viral activity relied on the recruitment of the ISGF3 components STAT1, STAT2 and IRF9 in a phosphorylation- and time-dependent manner. Likewise, in ST2-U3C and Huh-STAT1KO cells lacking STAT1, ISG expression correlated with DNA-binding of phosphorylated STAT2/IRF9. This pointed to a dominant role of classical ISGF3 and STAT2/IRF9, and not U-ISGF3 or U-STAT2/IRF9, in the regulation of early and prolonged ISG expression and viral protection, in WT and STAT1-KO cells. In addition, comparative experiments in U3C (STAT1-KO) cells overexpressing all ISGF3 components (ST1-ST2-IRF9-U3C), revealed a threshold-dependent role of U-ISFG3, and potentially U-STAT2/IRF9, in the regulation of constitutive and possibly long-term IFNα-treated ISG expression and anti-viral activity.
|
| |
|
| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for 2fTGH, ST2-U3C, Huh7.5, and Huh STAT1KO cells treated with IFN alpha
|
| |
|
| Contributor(s) |
Bluyssen HA, Nowicka H |
| Citation(s) |
38139463 |
| Submission date |
Nov 14, 2023 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Hans A.R. Bluyssen |
| E-mail(s) |
h.bluyss@amu.edu.pl
|
| Phone |
+48 061 8295832
|
| Organization name |
Adam Mickiewicz University
|
| Department |
Laboratory of Human Molecular Genetics
|
| Street address |
Uniwersytetu Poznańskiego 6
|
| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
| |
|
| Platforms (5)
|
| GPL15456 |
Illumina HiScanSQ (Homo sapiens) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
|
| Samples (89)
|
| GSM7899483 |
2fTGH,untreated,IRF9,rep1 |
| GSM7899484 |
2fTGH,untreated,IRF9,rep2 |
| GSM7899485 |
2fTGH,interferon alpha,2h,IRF9,rep1 |
| GSM7899486 |
2fTGH,interferon alpha,2h,IRF9,rep2 |
| GSM7899487 |
2fTGH,interferon alpha,24h,IRF9,rep1 |
| GSM7899488 |
2fTGH,interferon alpha,24h,IRF9,rep2 |
| GSM7899489 |
2fTGH,interferon alpha,72h,IRF9,rep1 |
| GSM7899491 |
2fTGH,interferon alpha,72h,IRF9,rep2 |
| GSM7899492 |
2fTGH,untreated,phospho-STAT1 |
| GSM7899493 |
2fTGH,interferon alpha,2h,phospho-STAT1 |
| GSM7899494 |
2fTGH,interferon alpha,24h,phospho-STAT1 |
| GSM7899495 |
2fTGH,interferon alpha,72h,phospho-STAT1 |
| GSM7899496 |
2fTGH,untreated,STAT1,rep1 |
| GSM7899497 |
2fTGH,untreated,STAT1,rep2 |
| GSM7899499 |
2fTGH,interferon alpha,2h,STAT1,rep1 |
| GSM7899500 |
2fTGH,interferon alpha,2h,STAT1,rep2 |
| GSM7899501 |
2fTGH,interferon alpha,2h,STAT1,rep3 |
| GSM7899502 |
2fTGH,interferon alpha,24h,STAT1,rep1 |
| GSM7899504 |
2fTGH,interferon alpha,24h,STAT1,rep2 |
| GSM7899505 |
2fTGH,interferon alpha,72h,STAT1,rep1 |
| GSM7899506 |
2fTGH,interferon alpha,72h,STAT1,rep2 |
| GSM7899508 |
2fTGH,untreated,phospho-STAT2 |
| GSM7899509 |
2fTGH,interferon alpha,2h,phospho-STAT2 |
| GSM7899510 |
2fTGH,interferon alpha,24h,phospho-STAT2 |
| GSM7899512 |
2fTGH,interferon alpha,72h,phospho-STAT2 |
| GSM7899513 |
2fTGH,untreated,STAT2,rep1 |
| GSM7899514 |
2fTGH,untreated,STAT2,rep2 |
| GSM7899516 |
2fTGH,interferon alpha,2h,STAT2,rep1 |
| GSM7899517 |
2fTGH,interferon alpha,2h,STAT2,rep2 |
| GSM7899518 |
2fTGH,interferon alpha,2h,STAT2,rep3 |
| GSM7899519 |
2fTGH,interferon alpha,2h,STAT2,rep4 |
| GSM7899521 |
2fTGH,interferon alpha,24h,STAT2,rep1 |
| GSM7899522 |
2fTGH,interferon alpha,24h,STAT2,rep2 |
| GSM7899523 |
2fTGH,interferon alpha,72h,STAT2,rep1 |
| GSM7899525 |
2fTGH,interferon alpha,72h,STAT2,rep2 |
| GSM7899526 |
ST2-U3C,untreated,IRF9,rep1 |
| GSM7899527 |
ST2-U3C,untreated,IRF9,rep2 |
| GSM7899528 |
ST2-U3C,untreated,IRF9,rep3 |
| GSM7899529 |
ST2-U3C,interferon alpha,2h,IRF9,rep1 |
| GSM7899531 |
ST2-U3C,interferon alpha,2h,IRF9,rep2 |
| GSM7899532 |
ST2-U3C,interferon alpha,2h,IRF9,rep3 |
| GSM7899533 |
ST2-U3C,interferon alpha,24h,IRF9,rep1 |
| GSM7899535 |
ST2-U3C,interferon alpha,24h,IRF9,rep2 |
| GSM7899536 |
ST2-U3C,interferon alpha,24h,IRF9,rep3 |
| GSM7899537 |
ST2-U3C,interferon alpha,72h,IRF9,rep1 |
| GSM7899538 |
ST2-U3C,interferon alpha,72h,IRF9,rep2 |
| GSM7899540 |
ST2-U3C,untreated,phospho-STAT2,rep1 |
| GSM7899541 |
ST2-U3C,untreated,phospho-STAT2,rep2 |
| GSM7899543 |
ST2-U3C,interferon alpha,2h,phospho-STAT2,rep1 |
| GSM7899544 |
ST2-U3C,interferon alpha,2h,phospho-STAT2,rep2 |
| GSM7899545 |
ST2-U3C,interferon alpha,72h,phospho-STAT2,rep1 |
| GSM7899547 |
ST2-U3C,interferon alpha,72h,phospho-STAT2,rep2 |
| GSM7899548 |
ST2-U3C,untreated,STAT2,rep1 |
| GSM7899549 |
ST2-U3C,untreated,STAT2,rep2 |
| GSM7899550 |
ST2-U3C,interferon alpha,2h,STAT2,rep1 |
| GSM7899552 |
ST2-U3C,interferon alpha,2h,STAT2,rep2 |
| GSM7899553 |
ST2-U3C,interferon alpha,2h,STAT2,rep3 |
| GSM7899554 |
ST2-U3C,interferon alpha,24h,STAT2,rep1 |
| GSM7899555 |
ST2-U3C,interferon alpha,24h,STAT2,rep2 |
| GSM7899557 |
ST2-U3C,interferon alpha,72h,STAT2,rep1 |
| GSM7899558 |
ST2-U3C,interferon alpha,72h,STAT2,rep2 |
| GSM7899559 |
Huh7.5 STAT1 K.O.,untreated,IRF9,rep1 |
| GSM7899561 |
Huh7.5 STAT1 K.O.,untreated,IRF9,rep2 |
| GSM7899562 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,IRF9,rep1 |
| GSM7899563 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,IRF9,rep2 |
| GSM7899565 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,IRF9,rep1 |
| GSM7899566 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,IRF9,rep2 |
| GSM7899567 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,IRF9,rep1 |
| GSM7899569 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,IRF9,rep2 |
| GSM7899570 |
Huh7.5 STAT1 K.O.,untreated,pSTAT2,rep1 |
| GSM7899571 |
Huh7.5 STAT1 K.O.,untreated,pSTAT2,rep2 |
| GSM7899573 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,pSTAT2,rep1 |
| GSM7899574 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,pSTAT2,rep2 |
| GSM7899575 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,pSTAT2,rep1 |
| GSM7899577 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,pSTAT2,rep2 |
| GSM7899578 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,pSTAT2,rep1 |
| GSM7899580 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,pSTAT2,rep2 |
| GSM7899581 |
Huh7.5 STAT1 K.O.,untreated,STAT2,rep1 |
| GSM7899582 |
Huh7.5 STAT1 K.O.,untreated,STAT2,rep2 |
| GSM7899584 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,STAT2,rep1 |
| GSM7899585 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,STAT2,rep2 |
| GSM7899586 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,STAT2,rep1 |
| GSM7899588 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,STAT2,rep2 |
| GSM7899589 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,STAT2,rep1 |
| GSM7899591 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,STAT2,rep2 |
| GSM7899592 |
Huh7.5 STAT1 K.O.,untreated,input |
| GSM7899593 |
Huh7.5 STAT1 K.O.,interferon alpha,2h,input |
| GSM7899595 |
Huh7.5 STAT1 K.O.,interferon alpha,24h,input |
| GSM7899596 |
Huh7.5 STAT1 K.O.,interferon alpha,72h,input |
|
| This SubSeries is part of SuperSeries: |
| GSE247728 |
ISGF3 and STAT2/IRF9 direct basal and IFN-induced transcription through genome-wide binding of phosphorylated and unphosphorylated complexes to commonly ISRE containing ISGs |
|
| Relations |
| BioProject |
PRJNA1040217 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE247724_HuhST1KO_IFNa_24h_IRF9_idr.optimal_peak.regionPeak.txt.gz |
199.6 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_24h_STAT2_idr.optimal_peak.regionPeak.txt.gz |
362.1 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_24h_pSTAT2_idr.optimal_peak.regionPeak.txt.gz |
515.2 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_2h_IRF9_idr.optimal_peak.regionPeak.txt.gz |
8.3 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_2h_STAT2_idr.optimal_peak.regionPeak.txt.gz |
296.6 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_2h_pSTAT2_idr.optimal_peak.regionPeak.txt.gz |
344.5 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_72h_IRF9_idr.optimal_peak.regionPeak.txt.gz |
191.3 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_72h_STAT2_idr.optimal_peak.regionPeak.txt.gz |
388.4 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_IFNa_72h_pSTAT2_idr.optimal_peak.regionPeak.txt.gz |
608.0 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_UN_IRF9_idr.optimal_peak.regionPeak.txt.gz |
5.1 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_UN_STAT2_idr.optimal_peak.regionPeak.txt.gz |
21.0 Kb |
(ftp)(http) |
TXT |
| GSE247724_HuhST1KO_UN_pSTAT2_rep1_vs_rep2.idr0.05.regionPeak.txt.gz |
203 b |
(ftp)(http) |
TXT |
| GSE247724_RAW.tar |
8.9 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...