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Series GSE79519 Query DataSets for GSE79519
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 [RNA-seq]
Organism Mus musculus
Experiment type Expression 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 Mouse pro-B Ba/F3 cells treated with lentiviral vectors expressing short-hairpins to knock-down various genes (STAT5a, STAT5b, LSD1 and HDAC3). All KDs were analysed versus cells treated with lentiviral construct expressing a No-Target short-hairpin at the same condition (either minus [IL3 deprivation for 6h] or plus [IL3 deprivation for 6h and IL3 stimulation for 30min]). Wild-type cells were also generated and compared between the two conditions. All samples contain biological replicates (3-5 depending on the sample).
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 (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (27)
GSM2096655 RNA-seq_wtBaFminus 1
GSM2096656 RNA-seq_wtBaFminus 2
GSM2096657 RNA-seq_wtBaFminus 3
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 PRJNA316076
SRA SRP072209

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

Supplementary file Size Download File type/resource
GSE79519_DESeq2_shHDAC3_vs_shNT_plus.xlsx 2.0 Mb (ftp)(http) XLSX
GSE79519_DESeq2_shLSD1_vs_shNT_plus.xlsx 2.0 Mb (ftp)(http) XLSX
GSE79519_DESeq2_shSTAT5a_vs_shNT_plus.xlsx 1.9 Mb (ftp)(http) XLSX
GSE79519_DESeq2_shSTAT5b_vs_shNT_plus.xlsx 2.0 Mb (ftp)(http) XLSX
GSE79519_DESeq2_wtBaFplus_vs_wtBaFminus.xlsx 2.1 Mb (ftp)(http) XLSX
GSE79519_RAW.tar 2.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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