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Series GSE183739 Query DataSets for GSE183739
Status Public on Jun 27, 2022
Title Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo [H2AK119ub CUT&RUN]
Platform organism Mus musculus
Sample organisms Drosophila melanogaster; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Parents transmit genetic and epigenetic information to their offspring. Maternal effect genes regulate the offspring epigenome to ensure normal development. Here we report that the epigenetic regulator SMCHD1 has a maternal effect on Hox gene expression and skeletal patterning. Maternal SMCHD1, present in the oocyte and preimplantation embryo, prevents precocious activation of Hox genes post-implantation. Without maternal SMCHD1, highly penetrant posterior homeotic transformations occur in the embryo. Hox genes are decorated with Polycomb marks H2AK119ub and H3K27me3 from the oocyte throughout early embryonic development; however, loss of maternal SMCHD1 does not deplete these marks. Therefore, we propose maternal SMCHD1 acts downstream of Polycomb marks to establish a chromatin state necessary for persistent epigenetic silencing and appropriate Hox gene expression later in the developing embryo. This is a striking role for maternal SMCHD1 in long-lived epigenetic effects impacting offspring phenotype.
 
Overall design H2AK119ub CUT&RUN-sequencing comparing Smchd1 wildtype and maternally deleted samples in 3 mESC lines grown in 2i+LIF medium for each genotype, and a differentiation timecourse with 2 replicate mESC of each genotype, each with 1-2 technical replicates. Note that no Ab control files are in H3K27me3_CUT_RUN_differentiation folder. Please add to current geo entry GSE183739 and update the experimental design with this description.
 
Contributor(s) Benetti N, Blewitt ME
Citation(s) 35879318
Submission date Sep 08, 2021
Last update date Nov 29, 2022
Contact name Natalia Benetti
E-mail(s) nataliabenetti17@gmail.com
Organization name WEHI
Street address 1G Royal Parade
City Parkville
State/province Victoria
ZIP/Postal code 3052
Country Australia
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (28)
GSM5569999 H2AK119ub CUT&RUN wt mESC line 1
GSM5570000 H2AK119ub CUT&RUN wt mESC line 2
GSM5570001 H2AK119ub CUT&RUN wt mESC line 3
This SubSeries is part of SuperSeries:
GSE183740 Maternal Smchd1 regulates Hox gene expression and patterning in the mouse embryo
Relations
Reanalysis of GSM4929375
Reanalysis of GSM4929381
BioProject PRJNA761783
SRA SRP336257

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
GSE183739_benetti_CUT_RUN_H2AK119ub.txt.gz 703.7 Kb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_2i_wt_vs_matdel.txt.gz 87.9 Kb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2.5_wt_vs_matdel.txt.gz 2.7 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_d2_wt_vs_matdel.txt.gz 15.7 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_d3_wt_vs_matdel.txt.gz 11.7 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2.5_vs_d3.txt.gz 15.7 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d2.5.txt.gz 9.3 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_matdel_d2_vs_d3.txt.gz 12.6 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2.5_vs_d3.txt.gz 9.2 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d2.5.txt.gz 3.3 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_csaw_peaks_wt_d2_vs_d3.txt.gz 15.0 Mb (ftp)(http) TXT
GSE183739_benetti_H2AK119ub_CUT_RUN_diff_FPKM_over_MACS_peaks.txt.gz 3.4 Mb (ftp)(http) TXT
GSE183739_third-party_reanalysis_readme.txt 2.0 Kb (ftp)(http) TXT
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