CTCF ChIPseq of mouse uterus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA945440 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23880012.fastq.gz | Fastqsanger.gz | |||
| SRR23880013.fastq.gz | Fastqsanger.gz |
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Project description:Receptors for estrogen and progesterone frequently interact, via Cohesin/CTCF loop extrusion, at enhancers distal from regulated genes; CTCF is decreased or mutated in >20% of human endometrial tumors, indicating its importance in uterine homeostasis. To better understand how CTCF-mediated enhancer-gene interactions impact endometrial development and function, the Ctcf gene was selectively deleted in female reproductive tissues of mice. Prepubertal Ctcfd/d uterine tissue exhibited normal morphology, with a significant reduction in the number of uterine glands compared to those without Ctcf deletion (Ctcff/f mice). Post-pubertal Ctcfd/d uteri were hypoplastic with significant reduction in both the size of the endometrial stroma and number of glands. Transcriptional profiling revealed increased expression of stem cell molecules Lif, EOMES and Lgr5, and enhanced inflammation pathways following Ctcf deletion. Analysis of the response of the uterus to steroid hormone stimulation showed that the response of the uterus to estrogen was not impacted, but that CTCF deletion affects a subset of progesterone responsive genes. This finding indicates 1) mediators of P signaling remain functional following Ctcf deletion and 2) certain P regulated genes are sensitive to Ctcf deletion, suggesting they depend on gene-enhancer interactions that require CTCF. The P responsive genes altered by CTCF ablation included Ihh, Fst and Errfi1, as well as other genes involved in the regulation of critical processes including hormone response, transcription, and inhibition of tumor generation. Overall, our findings reveal that uterine Ctcf plays a key role in P dependent expression of uterine genes underlying optimal post pubertal uterine development.
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Project description:CTCF is a highly conserved and ubiquitously expressed protein involved in several fundamental processes such as fine-tuning gene expression, imprinting, X-chromosome inactivation and 3D chromatin organisation. To understand the impact of differences in the concentration of CTCF abundance on these processes, we exploit a CTCF hemizygous mouse model with a stable reduction in the concentration of this protein. We derived twelve independent primary lines of mouse embryonic fibroblasts (MEFs) from six wildtype and six CTCF-hemizygous mouse E13.5 embryos. Total RNA from each MEF line was purified using QIAzol Lysis Reagent (Qiagen); DNase treatment and removal was performed using the TURBO DNA-freeTM Kit (Ambion, Life Technologies). Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumna HiSeq4000 to produce 150bp paired-end reads. On the same MEF lines we have performed ChIPseq for CTCF, H3K4me3 and H3K27ac and HiC.
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Project description:CTCF is a highly conserved and ubiquitously expressed protein involved in several fundamental processes such as fine-tuning gene expression, imprinting, X-chromosome inactivation and 3D chromatin organisation. To understand the impact of differences in the concentration of CTCF abundance on these processes, we exploit a CTCF hemizygous mouse model with a stable reduction in the concentration of this protein. We derived independent primary lines of mouse embryonic fibroblasts (MEFs) from wildtype and CTCF-hemizygous mouse E13.5 embryos. For three biological replicates, cells were fixed in DMEM containing 2% fresh formaldehyde and incubated at room temperature for 10 min, quenched with 1M glycine for 5 min, and washed twice with ice cold PBS, before being flash-frozen at -80°C. Cross-linked cells were lysed, followed by chromatin HindIII digestion, biotinylataion, ligation, proteinase K treatment, DNA purification, sonication, end repair, biotin pull-down, adapter ligation, and PCR amplification. Pooled indexed libraries were sequenced on an Illumina HiSeq4000 to produce paired-end 150bp reads. On the same MEF lines we have performed RNAseq and ChIPseq for CTCF, H3K4me3 and H3K27ac.
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