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Series GSE136422 Query DataSets for GSE136422
Status Public on Jan 21, 2020
Title CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions [ChIP-seq]
Organisms Drosophila melanogaster; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Appropriate developmental gene regulation relies on the capacity of gene promoters to integrate inputs from distal regulatory elements, yet how this is achieved remains poorly understood. In embryonic stem cells (ESCs), a subset of silent developmental gene promoters are primed for activation by FBXL19, a CpG island binding protein, through its capacity to recruit CDK-Mediator. How mechanistically these proteins function together to prime genes for activation during differentiation is unknown. Here we discover that in mouse ESCs FBXL19 and CDK-Mediator support long-range interactions between silent gene promoters that rely on FBXL19 for their induction during differentiation and gene regulatory elements. During gene induction, these distal regulatory elements behave in an atypical manner, in that the majority do not acquire histone H3 lysine 27 acetylation and no longer interact with their target gene promoter following gene activation. Despite these atypical features, we demonstrate by targeted deletions that these distal elements are required for appropriate gene induction during differentiation. Together these discoveries demonstrate that CpG-island associated gene promoters can prime genes for activation by communicating with atypical distal gene regulatory elements to achieve appropriate gene expression.

Overall design Mouse embryonic stem cells in which the CxxC domain of Fbxl19 can be conditionally ablated (Dimitrova et al., eLIFE 290018), were profiled for H3K27ac using spike-in calibrated native ChIP-seq before or after retinoic acid-mediated differentiation

Please note that each * file was generated from both replicates and is linked to the corresponding rep1 sample records.
Contributor(s) Feldmann A, Dimitrova E, Kenney A, Klose RJ
Citation(s) 31996894
Submission date Aug 27, 2019
Last update date Apr 07, 2020
Contact name Angelika Feldmann
Phone 7983705260
Organization name University of Oxford, Department of Biochemistry
Street address South Parks Road
City Oxford
State/province England
ZIP/Postal code OX1 3QU
Country United Kingdom
Platforms (1)
GPL25537 Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus)
Samples (16)
GSM4048815 FBXL19fl_ES_UNT_rep1_ChIP_H3K27ac
GSM4048816 FBXL19fl_ES_UNT_rep2_ChIP_H3K27ac
GSM4048817 FBXL19fl_ES_TAM_rep1_ChIP_H3K27ac
This SubSeries is part of SuperSeries:
GSE136424 CDK-Mediator and FBXL19 cooperate in the induction of developmental genes by promoting regulatory interactions
BioProject PRJNA562780
SRA SRP219713

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
GSE136422_RAW.tar 2.7 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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