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Series GSE64767 Query DataSets for GSE64767
Status Public on Dec 09, 2015
Title Epigenetic Program and Transcription Factor Circuitry of Dendritic Cell Development
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells through successive steps of lineage commitment and differentiation. Multipotent progenitors (MPP) are committed to DC restricted common DC progenitors (CDP), which differentiate into specific DC subsets, classical DC (cDC) and plasmacytoid DC (pDC). To determine epigenetic states and regulatory circuitries during DC differentiation, we measured consecutive changes of genome-wide gene expression, histone modification and transcription factor occupancy during the sequel MPP-CDP-cDC/pDC. Specific histone marks in CDP reveal a DC-primed epigenetic signature, which is maintained and reinforced during DC differentiation. Epigenetic marks and transcription factor PU.1 occupancy increasingly coincide upon DC differentiation. By integrating PU.1 occupancy and gene expression we devised a transcription factor regulatory circuitry for DC commitment and subset specification. The circuitry provides the transcription factor hierarchy that drives the sequel MPP-CDP-cDC/pDC, including Irf4, Irf8, Tcf4, Spib and Stat factors. The circuitry also includes feedback loops inferred for individual or multiple factors, which stabilize distinct stages of DC development and DC subsets. In summary, here we describe the basic regulatory circuitry of transcription factors that drives DC development.
 
Overall design H3K4me3, H3K9me3 and H3K27me3 occupancy in MPP, CDP, cDC and pDC.
The ChIP-seq profiles are visualized by a customized UCSC genome browser track hub (http://www.molcell.rwth-aachen.de/dc/).
 
Contributor(s) Lin Q, Chauvistré H, Costa IG, Gusmão EG, Mitzka S, Haenzelmann S, Baying B, Klisch T, Moriggl R, Hennuy B, Smeets H, Hoffmann K, Benes V, Seré K, Zenke M
Citation(s) 26476451
Submission date Jan 07, 2015
Last update date Mar 17, 2019
Contact name Martin Zenke
E-mail Martin.Zenke@rwth-aachen.de
Phone +49-241-80 80760
Organization name Institute for Biomedical Engineering
Department Cell Biology
Street address Universitatsklinikum Aachen, RWTH
City Aachen
State/province NRW
ZIP/Postal code 52074
Country Germany
 
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1384939 MPP_H3K4me3
GSM1384940 CDP_H3K4me3
GSM1384941 cDC_H3K4me3
Relations
BioProject PRJNA271821
SRA SRP051906

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
GSE64767_RAW.tar 2.8 Gb (http)(custom) TAR (of WIG)
Raw data are available in SRA
Processed data provided as supplementary file

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