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Series GSE242974 Query DataSets for GSE242974
Status Public on Sep 14, 2023
Title The role of SMC3 in heart development by regulating super-enhancer associated genes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Abnormal cardiac development has been observed in individuals with Cornelia de Lange Syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. But the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed an association between SMC3 mutations and congenital heart disease (CHD) in CdLS patients. To further explore this relationship, we utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which displayed varying degrees of outflow tract (OFT) abnormalities. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. Employing single nucleus RNA sequencing and 3C-high-throughput genome-wide translocation sequencing, we unveiled that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SE) and promoters. Notable, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research uncovers a novel role for SMC3 in heart development by regulating SE-associated genes, suggesting its potential relevance as one of the CHD-related genes and providing crucial insights into the molecular basis of cardiac development.
Overall design Transcriptome profiles and pair-wise chromatin interactions of diverse cell types were examined from different viewpoints respectively before or/and after SMC3 knock down (duplicates), respectively.
Contributor(s) Zhang B, Zhu Y, Dai R
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Submission date Sep 12, 2023
Last update date Sep 14, 2023
Contact name bowen zhang
Phone 13399288269
Organization name Fudan university
Street address dongan road
City shanghai
State/province shanghai
ZIP/Postal code 200032
Country China
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (35)
GSM7776329 HL-1-SMC3-KD-ETS2-3C-HTGTS-rep1
GSM7776330 HL-1-SMC3-KD-ETS2-3C-HTGTS-rep2
GSM7776331 HL-1-SMC3-NC-ETS2-3C-HTGTS-rep1
BioProject PRJNA1015646

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
GSE242974_Ets2-SE-gene_count_matrix.xlsx 2.8 Mb (ftp)(http) XLSX
GSE242974_RAW.tar 738.0 Mb (http)(custom) TAR (of BED, BEDGRAPH, BW)
GSE242974_Smc3-All.ReadsCount.xls.gz 2.5 Mb (ftp)(http) XLS
GSE242974_barcodes.tsv.gz 120.8 Kb (ftp)(http) TSV
GSE242974_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSE242974_matrix.mtx.gz 179.3 Mb (ftp)(http) MTX
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