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Series GSE46044 Query DataSets for GSE46044
Status Public on Sep 09, 2013
Title A compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupy CBF-MYH11/RUNX1 target genes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Different mechanisms for CBF-MYH11 function in acute myeloid Leukemia (AML) with inv(16) have been proposed such as tethering of RUNX1 outside the nucleus, interference with transcription factor complex assembly and recruitment of histone deacetylases, all resulting in transcriptional repression of RUNX1 target genes. Here, through genome-wide CBF-MYH11 binding site analysis and quantitative interaction proteomics we found that CBF-MYH11 localizes to RUNX1 occupied promoters where it interacts with TAL1, FLI1 and TBP associated factors (TAFs) in the context of the hematopoietic transcription factors ERG, GATA2 and PU.1/SPI1 and the co regulators EP300 and HDAC1. Transcriptional analysis revealed that upon fusion protein knock down a subset of the CBF-MYH11 target genes show increased expression, confirming a role in transcriptional repression. However, the majority of CBF-MYH11 target genes, including genes implicated in hematopoietic stem cell (HSC) self-renewal such as ID1, LMO1 and JAG1, are actively transcribed and upon fusion protein knock down repressed. Together these results suggest an essential role for CBF-MYH11 in regulating expression of genes involved in maintaining a stem cell phenotype.
Overall design 17 ChIP-seq samples using antibodies recognizing the indicated proteins and one RNA-seq file from ME-1 cells were analyzed. In addition 2 ChIP-seq profiles were generated using patient AML cells. A CBFβ-MYH11 inducible U937 system (U937CM) was used to examine binding patterns before (1 profile) and after (2 profiles) induction of CBFb-MYH11. In addition, expression was measured through RNA-seq analysis of the two states. The U937CM cells were maintained in the presence of tetracyclin (Tet, 1 uM) and grown in the absence of tetracycline for 3 days to induce expression of CBFβ-MYH11. Finally, a CBFb-MYH11 knock down system was developed in ME-1 cells. Two ME-1 cell lines were created, one with a stably integrated shRNA construct that targets CBFb-MYH11 (ME-1_knockdown) and one with a scrambled shRNA construct (ME-1_SCR). Expression of the shRNA constructs was induced using doxycyclin (dox; 1 mM) treatment for 3 days.
Contributor(s) Mandoli A, Singh AA, Jansen PW, Wierenga B, Riahi H, Franci G, Prange K, Saeed S, Vellenga E, Vermeulen M, Stunnenberg HG, Martens JH
Citation(s) 24002588
Submission date Apr 15, 2013
Last update date Nov 11, 2021
Contact name Joost Martens
Phone 0243780645
Organization name Radboud University
Department RIMLS
Lab Molecular Biology
Street address Geert Grooteplein 28
City Nijmegen
State/province Nederland
ZIP/Postal code 6525GA
Country Netherlands
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (27)
GSM1122302 ME-1, CBFb_SC ChIP-Seq
GSM1122303 ME-1, CBFb_A1329 ChIP-Seq
GSM1122304 ME-1, MYH11_Novous ChIP-Seq
BioProject PRJNA197000
SRA SRP021072

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Supplementary file Size Download File type/resource
GSE46044_RAW.tar 3.1 Gb (http)(custom) TAR (of BEDGRAPH, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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