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Series GSE107553 Query DataSets for GSE107553
Status Public on Feb 07, 2018
Title Cistrome analysis of SKI and RUNX1 in HL60
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary SKI is a transcriptional co-regulator and overexpressed in various human tumors, for example in acute myeloid leukemia (AML). SKI contributes to the origin and maintenance of the leukemic phenotype. Here we use ChIP-seq and RNA-seq to identify the epigenetic alterations induced by SKI overexpression in AML cells. We show that approximately two thirds of differentially expressed genes are up-regulated upon SKI deletion, of which nearly 50% harbour SKI binding sites in their proximity, primarily in enhancer regions. Gene ontology analysis reveals that many of the differentially expressed genes are annotated to hematopoietic cell differentiation and inflammatory response, corroborating our finding that SKI deletion causes a release of the myeloid differentiation block in HL60 cells. We find that SKI peaks are enriched for RUNX1 consensus motifs, particularly in up-regulated SKI targets. RUNX1 ChIP-seq demonstrates that nearly 70% of RUNX1 binding sites overlap with SKI peaks, mainly at enhancer regions. SKI and RUNX1 co-occupy the same genomic sites and cooperate in gene silencing. Our work demonstrates for the first time on a genome-wide scale the predominant co-repressive function of SKI in AML cells and uncovers the transcription factor RUNX1 as an important mediator of SKI-dependent transcriptional repression.
Overall design Examining of SKI genome-wide binding and its comparison with other transcription factors and histone modifications.
Contributor(s) Feld C, Sahu P, Stiewe T, Neubauer A, Bauer UM
Citation(s) 29471413
Submission date Nov 30, 2017
Last update date May 15, 2019
Contact name Uta Maria Bauer
Organization name Philipps University Marburg
Department Institute of Molecular Biology and Tumor Research
Lab AG Bauer
Street address Hans-Meerwein-Str. 2
City Marburg
State/province Hessen
ZIP/Postal code 35043
Country Germany
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (14)
GSM2871145 HL60_WT_IgG
GSM2871146 HL60_CTR-1_IgG
GSM2871147 HL60_KO-3_IgG
This SubSeries is part of SuperSeries:
GSE107556 Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1
BioProject PRJNA420513
SRA SRP125911

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Supplementary file Size Download File type/resource
GSE107553_RAW.tar 1.7 Gb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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