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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
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
BioProject PRJNA430300
SRA SRP131017

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Supplementary file Size Download File type/resource
GSE109251_RAW.tar 2.7 Mb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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