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Series GSE69905 Query DataSets for GSE69905
Status Public on Jun 02, 2016
Title 5-hydroxymethylcytosine poises expression of genes involved in hematopoietic differentiation
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Epigenetic processes regulate hematopoietic stem cell homeostasis. The recent discovery of 5-hydroxymethylcytosine (5hmC) provides new insights into the epigenetic regulation of gene expression during development. We used reduced representation of 5-hydroxymethylcytosine profiling (RRHP) to characterize the genome-wide distribution of 5hmC in human CD34+ hematopoietic stem/progenitor cells, lymphocytes, monocytes and granulocytes. We show that 5hmC levels decrease during cell differentiation and that 5hmC is associated with H3K4me1 and H3K27ac histone modifications, indicative of active enhancers. In CD34+ cells, the presence of 5hmC at presumed active enhancers correlates with increased binding of RUNX1 and FLI1, two transcription factors essential for hematopoiesis. Moreover, in progenitor cells, 5hmC poises the expression of transcription factors regulating hematopoietic lineage commitment, such as RUNX1, FOXO1 and C/EBP-alpha. Our study provides the first comprehensive genome-wide overview of 5hmC distribution in human hematopoietic cells and of its potential role in transcriptional network regulation during hematopoiesis.
 
Overall design RRHP: profiling of 5-hydroxymethylcytosine and RNA-seq in human blood cells
 
Contributor(s) Tekpli X, Staerk J
Citation(s) 27252783
Submission date Jun 16, 2015
Last update date May 15, 2019
Contact name Xavier Tekpli
E-mail(s) xavier.tekpli@hotmail.fr
Organization name Institute for Cancer Research
Department Department of Genetics
Street address Montebello
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (14)
GSM1712255 RRHP_CB_CD34+_348
GSM1712256 RRHP_CB_CD34+_350
GSM1712257 RRHP_BM_CD34+
Relations
BioProject PRJNA287113
SRA SRP059530

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
GSE69905_RAW.tar 97.4 Mb (http)(custom) TAR (of BED, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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