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SuperSeries Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE174528 | GEO | 2021/05/17

REPOSITORIES: GEO

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping.

Project description:Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated chromatin loop structures. To understand CTCF's direct role in global transcriptional regulation, we integrated the miniAID-mClover3 cassette to the endogenous CTCF locus in a human pediatric B-ALL cell line, SEM, and an immortal erythroid precursor cell line, HUDEP-2, to allow for acute depletion of CTCF protein by the auxin-inducible degron system. In SEM cells, CTCF loss notably disrupted intra-TAD loops and TAD integrity in concurrence with a reduction in CTCF-binding affinity, while showing no perturbation to nuclear compartment integrity. Strikingly, the overall effect of CTCF's loss on transcription was minimal. Whole transcriptome analysis showed hundreds of genes differentially expressed in CTCF-depleted cells, among which MYC and a number of MYC target genes were specifically downregulated. Mechanically, acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ∼1.8 Mb downstream. Notably, MYC expression was not profoundly affected upon CTCF loss in HUDEP-2 cells suggesting that CTCF could play a B-ALL cell line specific role in maintaining MYC expression.

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping

Project description:In human cells, CTCF’s role in genomic organization and global transcription regulation is less clearly defined due to the lack of available tools to efficiently deplete CTCF. Here, we used an auxin-inducible degron system to conditionally deplete CTCF in a human B-cell lymphoblastic leukemia (B-ALL) cell line, SEM. Cut & Run ChIP-seq showed acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ~1.8 Mb downstream.

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SuperSeries Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

Project description:SuperSeries Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping

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Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

Project description:Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping