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Series GSE109251 Query DataSets for GSE109251
Status Public on Oct 22, 2019
Title Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage [FAIRE-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Although Tead4 is well-known to be critical for blastocyst development and trophoblast lineage differentiation, the higher-order chromatin organization around this gene remains poorly understood. We assayed long-range chromosomal interactions on the Tead4 promoter in mouse embryonic stem (ES) cells and trophoblast stem (TS) cells using the circular chromosome conformation capture (4C)-seq technique. We observed frequent overlaps of genomic regions interacting with the Tead4 promoter and open chromatin regions identified by FAIRE-seq in TS cells. By systematic reporter assays using ES and TS cells, we identified five genomic fragments possessing a TS-specific enhancer activity to the Tead4 promoter, consisting of two intra- and three inter-chromosomal loci relative to the Tead4 gene on chromosome 6. We established five mouse lines deleted with one of the five enhancer elements using CRISPR/Cas9 genome editing, and evaluated the effect of each of the enhancer deletions on the Tead4 gene expression at the blastocyst stage. We observed 35-50% decrease of the Tead4 expression in the blastocysts with heterozygous or homozygous deletion of an inter-chromosomally located enhancer on chromosome 19 compared to that in wild-type blastocysts, whereas the other four deletions did not affect the Tead4 expression level. Our results demonstrate that inter-chromosomal enhancer-promoter interaction bears a critical role in assuring the appropriate level of Tead4 gene expression at the trophoblast lineage specification.
 
Overall design FAIRE-seq was performed for mouse TS and ES cells.
 
Contributor(s) Tomikawa J, Nakabayashi K
Citation(s) 31777916
Submission date Jan 16, 2018
Last update date Jan 13, 2020
Contact name Kazuhiko Nakabayashi
E-mail(s) nakabaya-k@ncchd.go.jp
Organization name National Research Institute for Child Health and Development
Department Department of Maternal-Fetal Biology
Street address 2-10-1 Okura
City Setagaya
State/province Tokyo
ZIP/Postal code 157-8535
Country Japan
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (4)
GSM2935897 B6ES_FAIRE_Rep1
GSM2935898 B6ES_FAIRE_Rep2
GSM2935899 B6TS_FAIRE_Rep1
This SubSeries is part of SuperSeries:
GSE109252 Inter-chromosomal enhancer-promoter interaction critical for the appropriate level of Tead4 gene expression at the blastocyst stage
Relations
BioProject PRJNA430300
SRA SRP131017

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
GSE109251_RAW.tar 2.7 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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