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Series GSE79518 Query DataSets for GSE79518
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.
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.
Contributor(s) Nanou A, Katsantoni E
Citation(s) 27651463
Submission date Mar 23, 2016
Last update date May 15, 2019
Contact name Aikaterini Nanou
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)
GSM2096640 ChIP_STAT5Aminus 1
GSM2096641 ChIP_STAT5Aminus 2
GSM2096642 ChIP_STAT5Aplus 1
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.
BioProject PRJNA316077
SRA SRP072208

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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