|
| Status |
Public on Nov 30, 2016 |
| Title |
The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a dimer motif, and such binding induced activation or repression. Strong STAT5 binding was seen more frequently in intergenic regions, which might function as distal enhancer elements. Genes bound weakly by STAT5a and strongly by LSD1/HDAC3 present a STAT5a monomer like motif, and are differentially regulated based on their biological role, genomic binding localization and affinity. STAT5a binding in monomer like motifs was found with increased frequency in promoters, indicating a requirement for stabilization by additional factors, which might recruit LSD1/HDAC3. Our study describes an interaction network of STAT5a/LSD1/HDAC3 and a dual function of LSD1/HDAC3 on STAT5-dependent transcription, defined by protein-protein interactions, genomic binding positions-affinities and motifs.
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|
| Overall design |
ChIP-seq data in mouse pro-B Ba/F3 cells of 3 different factors (STAT5a, LSD1 and HDAC3) in two different conditions (minus [IL3 deprivation for 6h] and plus [IL3 deprivation for 6h and 30min IL3 stimulation]). Two biological replicates are included per factor and condition, and one Input sample of Ba/F3 cells.
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| |
|
| Contributor(s) |
Nanou A, Katsantoni E |
| Citation(s) |
27651463 |
| |
| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aikaterini Nanou |
| E-mail(s) |
ANanou@bioacademy.gr
|
| Phone |
+302106597396
|
| Organization name |
Biomedial Research Foundation Academy of Athens
|
| Department |
Hematology
|
| Lab |
Katsantoni Lab
|
| Street address |
Soranou Efessiou 4
|
| City |
Athens |
| State/province |
Attiki |
| ZIP/Postal code |
11527 |
| Country |
Greece |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (13)
|
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| This SubSeries is part of SuperSeries: |
| GSE79520 |
The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions. |
|
| Relations |
| BioProject |
PRJNA316077 |
| SRA |
SRP072208 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE79518_Merged_ChIPs_HDAC3minus.ANNOTATEDpeaks.xlsx |
682.3 Kb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_HDAC3minus.bedGraph.gz |
36.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_HDAC3minus.peaks.bed.gz |
41.1 Kb |
(ftp)(http) |
BED |
| GSE79518_Merged_ChIPs_HDAC3plus.ANNOTATEDpeaks.xlsx |
277.8 Kb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_HDAC3plus.bedGraph.gz |
42.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_HDAC3plus.peaks.bed.gz |
15.1 Kb |
(ftp)(http) |
BED |
| GSE79518_Merged_ChIPs_LSD1minus.ANNOTATEDpeaks.xlsx |
3.0 Mb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_LSD1minus.bedGraph.gz |
33.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_LSD1minus.peaks.bed.gz |
203.4 Kb |
(ftp)(http) |
BED |
| GSE79518_Merged_ChIPs_LSD1plus.ANNOTATEDpeaks.xlsx |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_LSD1plus.bedGraph.gz |
49.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_LSD1plus.peaks.bed.gz |
207.1 Kb |
(ftp)(http) |
BED |
| GSE79518_Merged_ChIPs_STAT5Aminus.ANNOTATEDpeaks.xlsx |
1.0 Mb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_STAT5Aminus.bedGraph.gz |
38.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_STAT5Aminus.peaks.bed.gz |
61.4 Kb |
(ftp)(http) |
BED |
| GSE79518_Merged_ChIPs_STAT5Aplus.ANNOTATEDpeaks.xlsx |
2.8 Mb |
(ftp)(http) |
XLSX |
| GSE79518_Merged_ChIPs_STAT5Aplus.bedGraph.gz |
39.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE79518_Merged_ChIPs_STAT5Aplus.peaks.bed.gz |
190.6 Kb |
(ftp)(http) |
BED |
| GSE79518_RAW.tar |
311.7 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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