GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE42108 Query DataSets for GSE42108
Status Public on Jul 11, 2016
Title NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome- wide chromatin dynamics and ChIP-seq to determine these transcription factors’ (TFs) activities in terminal megakaryocyte (MK) maturation. Enhancers with H3K4me2-marked nucleosome pairs were most enriched for NF-E2, FLI and RUNX sequence motifs, suggesting that this TF triad controls much of the late MK program. ChIP-seq revealed NF-E2 occupancy near previously implicated target genes, whose expression is compromised in Nfe2-null cells, and many other genes that become active late in MK differentiation. FLI and RUNX were also the motifs most enriched near NF-E2 binding sites and ChIP-seq implicated FLI1 and RUNX1 in activation of late MK, including NF-E2-dependent, genes. Histones showed limited activation in regions of single TF binding, while enhancers that bind NF-E2 and either RUNX1, FLI1 or both TFs gave the highest signals for TF occupancy and H3K4me2; these enhancers associated best with genes activated late in MK maturation. Thus, three essential TFs co- occupy late-acting cis-elements and show evidence for additive activity at genes responsible for platelet assembly and release. These findings provide a rich dataset of TF and chromatin dynamics in primary MK and explain why individual TF losses cause thrombopocytopenia.
Overall design ChIP-Seq of key transcription factors in matured megakaryocytes
Contributor(s) Zang C, Luyten A, Shivdasani RA, Liu XS
Citation(s) 27457419
Submission date Nov 07, 2012
Last update date May 15, 2019
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 (3)
GSM1032607 MK5D_Fli1
GSM1032608 MK5D_Runx1
GSM1032609 MK5D input
BioProject PRJNA179147
SRA SRP017109

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
GSE42108_RAW.tar 2.1 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap