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Series GSE131061 Query DataSets for GSE131061
Status Public on Apr 08, 2020
Title The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cell type diversity during neuro-ectodermal (NE) differentiation is achieved through selective activation and silencing of neurodevelopmental genes. Here, we show a key role for the histone deacetylase complex MiDAC during neuronal differentiation of mouse embryonic stem cells (mESCs) into NE. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC mediates the removal of H4K20ac on the promoters and enhancers of pro-neural genes such as the axon guidance ligands Slit3 and Ntn1 while in parallel reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis thereby upregulating and inhibiting gene expression, respectively. Furthermore, neurite outgrowth defects in MiDAC KO neurons can be rescued by restoring Slit3/Robo3-Ntn1/Unc5b signaling. Taken together, our work suggests a crucial role for MiDAC in regulating the secretome of the Slit3/Robo3-Ntn1/Unc5b signaling axes to ensure the proper integrity of neurite development.
 
Overall design ChIP-seq was carried out in mESCs for the histone modification marks H3K4me1, H3K4me3, H3K27ac, H3K27me3 and for Dnttip1, a subunit of MiDAC. ChIPs against each histone mark or Dnttip1 were carried out at least in duplicate for each genotype. Genotypes used were WT, Dnttip1 KO and Elmsan1 KO.
 
Contributor(s) Mondal B, Jin H, Kallappagoudar S, Sedkov Y, Martinez T, Sentmanat MF, Poet GJ, Li C, Fan Y, Pruett-Miller SM, Herz H
Citation(s) 32297854, 35820704
Submission date May 12, 2019
Last update date Aug 02, 2022
Contact name Hans-Martin Herz
E-mail(s) hans-martin.herz@stjude.org
Phone 901-595-2058
Organization name St. Jude Children's Research Hospital
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105-3678
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (32)
GSM3762881 WT_Input_PFA_rep1
GSM3762882 WT_Input_DCL_rep1
GSM3762883 WT_Input_DCL_rep2
This SubSeries is part of SuperSeries:
GSE131062 The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth
Relations
BioProject PRJNA542516
SRA SRP198174

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
GSE131061_RAW.tar 6.6 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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