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Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering

ABSTRACT: Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering

PROVIDER: PRJNA1280052 | ENA |

REPOSITORIES: ENA

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Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq]

Project description:We developed a panel of chimeric proteins consisting of either full-length or truncated CTCF fused with programmable DNA-binding module dCas9 and fluorescent tracker EGFP. We found that the recruitment of a chimeric protein based on the CTCF N-terminal domain and two zinc-finger domains to the human HOXD locus leads to the de novo formation of a spatial contact with a nearby cohesin/CTCF-bound region anchoring several chromatin loops. This chimeric protein did not show binding to CTCF motifs and did not affect epigenetic and transcription profile of the locus. Recruitment of this chimeric protein is also able to restore chromatin loops, lost after deletion of an endogenous CTCF binding site. Together, our data indicate that the ectopic recruitment of CTCF N-terminal part could be an appropriate tool for the 3D genome engineering.

2025-08-15 | GSE300307 | GEO

Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [RNA-seq]

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Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [Hi-C]

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Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [Hi-C]

Project description:Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [Hi-C]

| PRJNA1280054 | ENA

Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq]

Project description:Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [CHIP-seq]

| PRJNA1280070 | ENA

Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [RNA-seq]

Project description:Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering [RNA-seq]

| PRJNA1280056 | ENA

Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome Engineering

Project description: Not available

| S-EPMC12347799 | biostudies-literature

Ectopic recruitment of the CTCF N-terminal domain with two proximal zinc-finger domains as a tool for 3D genome engineering

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-08-15 | GSE300308 | GEO

Genome engineering with zinc-finger nucleases.

Project description: Not available

| S-EPMC3176093 | biostudies-literature

Off-Target Analysis of Zinc Finger Nucleases

Project description:Zinc Finger Nucleases (ZFNs) facilitate precise editing of DNA enabling targeted genomic modifications in vivo. ZFNs have been employed to obtain genetically modified plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double stranded breaks at off-target sites within the genome. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites within the zebrafish genome using Illumina sequencing. Only a minority of these off-target sites displayed significant lesion frequency with kdrl ZFNs. Furthermore, we find that active off-target sites appear to be defined by the thermodynamics of zinc finger-DNA recognition. Surprisingly, we observed that the zinc finger protein specificity and the choice of the engineered dimerization domain of the FokI nuclease could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both ZFP-dependent and –independent mechanisms of potential improvement for engineering ZFNs with higher levels of precision. Examined lesions at 141 off-target sites for various treatments of ZFNs and compare to the untreated sample stage 1: raw read but missing quality values stage 2: fastq files available from SRA

2010-08-25 | E-GEOD-23762 | biostudies-arrayexpress

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