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Series GSE81009 Query DataSets for GSE81009
Status Public on Dec 24, 2016
Title Global binding of isoforms of Wilms' Tumor gene 1 and H3K4me3 in K562 cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Background: Wilms' tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia (AML). A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (KTS), is believed to change the DNA binding affinity of WT1. Altered balance between WT1 -KTS and WT1 +KTS expression associates with poor prognosis in AML. Methods: We characterized the DNA binding patterns of biotin-tagged WT1 -KTS and WT1 +KTS in K562 cells by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Results: We discovered that WT1 -KTS preferentially binds near transcription start sites (TSS) and in enhancers, whereas WT1 +KTS binds within gene bodies. Additionally, we observed a significant overlap between WT1 -KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif analysis showed enrichment of two TRANSFAC derived motif matrices within peaks for both isoforms, and enrichment of several previously published WT1 motifs which, however, differed between isoforms. Additional analyses showed that WT1 -KTS and WT1 +KTS target genes are transcribed to a higher extent than non-targets, and involved in cell proliferation, cell death, and development. Conclusions: Our results provide the first evidence that WT1 -KTS and WT1 +KTS bind principally different regions of the genome, yet share target genes. Our results indicate isoform-specific regulation of processes related to cell proliferation and differentiation, consistent with the involvement of WT1 in AML.
Overall design Streptavidin capture of biotinylated WT1 –KTS (two replicates), biotinylated WT1 +KTS (three replicates) and background K562-BirA cells (three replicates; background control). H3K4me3 immunoprecipitation in cells containing biotinylated WT1 –KTS (three replicates) and in cells containing biotinylated WT1 +KTS (two replicates).
Contributor(s) Ullmark T, Järvstråt L
Citation(s) 27612989
Submission date May 02, 2016
Last update date May 15, 2019
Contact name Linnea Järvstråt
Organization name Lund University
Department Department of Hematology and Transfusion Medicine
Lab Björn Nilsson
Street address Klinikgatan 26
City Lund
State/province Scania
ZIP/Postal code 22184
Country Sweden
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (22)
GSM2140606 WT1minusKTS cells replicate 1 Streptavidin
GSM2140607 WT1minusKTS cells replicate 2 Streptavidin
GSM2140608 WT1plusKTS cells replicate 1 Streptavidin
BioProject PRJNA320271
SRA SRP074245

Download family Format
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Supplementary file Size Download File type/resource
GSE81009_RAW.tar 15.9 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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