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CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [4C-seq]

ABSTRACT: In this study, we performed 4C sequencing to investigate alterations in chromatin interactions mediated by the Lmod2 promoter and its potential enhancer.

ORGANISM(S): Mus musculus

PROVIDER: GSE276654 | GEO | 2025/04/09

REPOSITORIES: GEO

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CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

Project description:In this study, we analyzed gene expression change in heart tissues from 8-week-old wild-type and Ctcf heterozygous mutant mice by using RNA-seq.

2025-04-09 | GSE276744 | GEO

CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [4C-seq]

Project description:CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [4C-seq]

| PRJNA1158454 | ENA

CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.

Project description:The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explore the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibit growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single-cell transcriptome levels. This mutation induces premature stem-like cell exhaustion, accelerates the maturation of GABAergic neurons, and disrupts neurodevelopmental and synaptic pathways. Additionally, it specifically hinders CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrors the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.

| S-EPMC11217373 | biostudies-literature

Dissecting developmental disorders caused by CTCF mutation at R567 [4C]

Project description:In this study, we performed 4C sequencing experiments to investigate the change of chromatin interactions between the promoters of Pcdh genes and enhancers across cPcdh locus.

2024-05-06 | GSE214688 | GEO

CTCF mutation at R567 affects mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

Project description:In this study, we analyzed gene expression change in heart tissues from wild-type, Ctcf heterozygous and homozygous mutant mice by using RNA-seq.

2025-04-09 | GSE262508 | GEO

CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

Project description:CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

| PRJNA1158787 | ENA

Dissecting developmental disorders caused by CTCF mutation at R567 [4C]

Project description:Dissecting developmental disorders caused by CTCF mutation at R567 [4C]

| PRJNA886689 | ENA

CTCF mutation at R567 causes developmental disorders by 3D genome rearrangement, premature exhaustion of stem cells and abnormal neurodevelopment [scRNA-seq]

Project description:In this study, we performed single RNA sequencing in 1-month and 2-month cortical organoids derived from wild-type and Ctcf heterozygous hESCs.

2024-05-06 | GSE231847 | GEO

CTCF mutation at R567 affects mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

Project description:CTCF mutation at R567 affects mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

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CTCF binding polarity determines chromatin looping [4C]

Project description:CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure. 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells

2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress

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