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Series GSE42110 Query DataSets for GSE42110
Status Public on Jul 28, 2014
Title Epigenetic and transcriptional control in hematopoietic development and lineage differentiation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Hematopoiesis is a well-established model system to study molecular mechanisms of lineage-specific differentiation. Key transcription factors (TFs), such as PU.1, NF-E2 and GATA1 are implicated in crucial aspects of distinct hematopoietic lineages. How TFs collaborate with histone modificatons and how they affect the chromatin status remains to be elucidated. Chromatin-Immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been proven to be an excellent tool to study chromatin modifications genome-wide. In this study, ChIP-seq was used to investigate the H3K4me2 landscape at enhancers during hematopoietic differentiation, starting from the hematopoietic stem cell (HSC) up to the fully differentiated erythrocyte, megakaryocyte or granulocyte. Although cell morphology and gene expression profiles differ extensively in committed erythrocytes, megakaryocytes and granulocytes, the genomic landscape of H3K4me2 is surprisingly alike across the three cell types. Granulocytes, in particular, seem to display an ‘erythocyte-like’ chromatin pattern. Similar results were observed for another chromatin mark, H3K27ac. Unexpectedly, the common progenitors of erythrocytes and granulocytes do not display a similar chromatin pattern, excluding the idea that the H3K4me2 mark is placed early on during differentiation. These results also suggest that the chromatin state is probably not the determining factor for lineage differentiation, but that rather lineage specific TF binding is important. In agreement with this, mature megakaryocytes loose the H3K4me2 mark surrounding erythrocyte-specific genes. This might be explained because megakaryocytes and erythrocytes both express the lineage specific TFs GATA1 and NF-E2. Altogether, we show that committed granulocytes and erythrocytes display similar H3K4me2 and H3K27ac patterns, and that those marks alone cannot predict which genes will be expressed eventually.
Overall design Genomic ChIP-Seq on key transcription factors and histone modification marks in hematopoiesis
Contributor(s) Luyten A, Zang C, Shivdasani RA, Liu XS
Citation(s) 25128499, 27457419
Submission date Nov 07, 2012
Last update date Sep 21, 2020
Contact name Chongzhi Zang
Organization name University of Virginia
Street address P. O. Box 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (26)
GSM1032631 HSC_H3K4me2
GSM1032632 CMP_H3K4me2
GSM1032633 GMP_H3K4me2
BioProject PRJNA179148
SRA SRP017108

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
GSE42110_RAW.tar 12.9 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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