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DNA methylation insulates exons from CTCF loops with nuclear speckles (HiChIP)

ABSTRACT: CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

ORGANISM(S): Homo sapiens

PROVIDER: GSE217754 | GEO | 2024/11/11

REPOSITORIES: GEO

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DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

Project description:CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

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DNA methylation insulates exons from CTCF loops with nuclear speckles

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

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YY1 is a structural regulator of enhancer-promoter loops [HiChIP]

Project description:There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

2017-11-16 | GSE99519 | GEO

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