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Series GSE78708 Query DataSets for GSE78708
Status Public on Feb 02, 2017
Title Not All H3K4 methylations are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary The spatiotemporal regulation of gene expression is central for cell-lineage specification during embryonic development and is achieved through the combinatorial action of transcription factors/co-factors and the epigenetic states at cis-regulatory elements. Previously, we reported that Mll2 (KMT2B)/COMPASS is responsible for the implementation of H3K4me3 at promoters of bivalent genes. Here, we show that Mll2/COMPASS can also implements H3K4me3 at some of the non-TSS regulatory elements, a subset of which share epigenetic signatures of active enhancers. Our mechanistic studies reveal that the association of Mll2’s CXXC domain with CpG-rich regions plays an instrumental role for chromatin targeting and subsequent implementation of H3K4me3. Although Mll2/COMPASS is required for H3K4me3 implementation on thousands of sites, it appears to be essential for the expression of a subset of genes, including those functioning in the control of transcriptional programs during embryonic development, indicating that not all H3K4 trimethylations implemented by MLL2/COMPASS are functionally equivalent.

Overall design Characterization of H3K4me3 and Mll2 occupancy by ChIP-seq in mouse embryonic stem cells and identifying their role in gene expression and during differentiation by RNA-seq studies. A high resolution 4C-seq experiments involving two restriction digests (HindIII and NlaIII) were performed to investigate the interaction bewteen promoters of Prdm1 and Prdm14 (viewponts) and cis-regulatory elements whose H3K4me3 is catalyzed by Mll2 in mouse embryonic stem cells.
Contributor(s) Hu D, Gao X, Shilatifard A
Citation(s) 28157506
Submission date Feb 26, 2016
Last update date May 15, 2019
Contact name Ali Shilatifard
Organization name Northwestern University Feinberg School of Medicine
Department Department of Biochemistry and Molecular Genetics
Lab Shilatifard Lab
Street address 320 E Superior St
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (90)
GSM2073006 H3K4me3_Mll2_mCXXC_F1
GSM2073007 H3K4me3_Mll2_mCXXC_F4
GSM2073008 H3K4me3_Mll2_Y2602A_F1
BioProject PRJNA313293
SRA SRP070890

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Supplementary file Size Download File type/resource
GSE78708_RAW.tar 19.5 Gb (http)(custom) TAR (of BW, TXT, XLS)
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Raw data are available in SRA
Processed data provided as supplementary file

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