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Identification of enhancer-promoter contacts in squamous cancer cells [ChIP-seq]

ABSTRACT: Profiling the histone modification H3K27ac, the co-activator BRD4 and the transcription factor SOX2 in squamous cancer cell lines

ORGANISM(S): Homo sapiens

PROVIDER: GSE166231 | GEO | 2021/10/19

REPOSITORIES: GEO

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Identification of enhancer-promoter contacts in squamous cancer cells [HiChIP]

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Identification of enhancer-promoter contacts in squamous cancer cells

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Identification of enhancer-promoter contacts in squamous cancer cells

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2021-10-17 | GSE166234 | GEO

Identification of enhancer-promoter contacts in squamous cancer cells [RNA-seq]

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Effects of supercoiling on enhancer-promoter contacts.

Project description:Using Brownian dynamics simulations, we investigate here one of possible roles of supercoiling within topological domains constituting interphase chromosomes of higher eukaryotes. We analysed how supercoiling affects the interaction between enhancers and promoters that are located in the same or in neighbouring topological domains. We show here that enhancer-promoter affinity and supercoiling act synergistically in increasing the fraction of time during which enhancer and promoter stay in contact. This stabilizing effect of supercoiling only acts on enhancers and promoters located in the same topological domain. We propose that the primary role of recently observed supercoiling of topological domains in interphase chromosomes of higher eukaryotes is to assure that enhancers contact almost exclusively their cognate promoters located in the same topological domain and avoid contacts with very similar promoters but located in neighbouring topological domains.

| S-EPMC4176356 | biostudies-other

ChIP-seq for the identification of enhancer and super enhancers in Acute Myeloid Leukemia cells with a 3q-aberration

Project description:To infer enhancers and super enhancers in Acute Myeloid Leukemia (AML) Cell lines with a 3q-aberration we determined regions enriched for H3K27AC, H3K4ME3, H3K4ME1, P300, and BRD4 in MOLM1. Additionally we determined regions enriched for P300 and BRD4 in the cell line Mutz3 which also harbors a 3q-aberration. As an control we performed Chip-Seq to determine enrichment for BRD4 in K562, which overexpresses the proto-oncogene EVI1, but has no apparent 3q-aberration. Ultimately, the ChipSeq experiments were utilized to infer which enhancer or super enhancer drives the overexpression of EVI1 in AMLs with a 3q-aberration. Finally, the effect of the compound JQ1 on the inferred super enhancers and the overexpression of EVI1 is tested by treating the cell line MOLM1 for 6 hours and determining the residual binding of BRD4.

2014-04-03 | E-MTAB-2224 | biostudies-arrayexpress

The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.

Project description:BackgroundRobustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers.ResultsUsing Hi-C data in multiple cell lines, we report a comprehensive map of promoters and active enhancers connected by chromatin contacts, spanning 9000 enhancer chains in 4 human cell lines associated with 2600 human genes. We find that the first enhancer in a chain that directly contacts the target promoter is commonly located at a greater genomic distance from the promoter than the second enhancer in a chain, 96 kb vs. 45 kb, respectively. The first enhancer also features higher similarity to the promoter in terms of tissue specificity and higher enrichment of loop factors, suggestive of a stable primary contact with the promoter. In contrast, a chain of enhancers which connects to the target promoter through a neutral DNA segment instead of an enhancer is associated with a significant decrease in target gene expression, suggesting an important role of the first enhancer in initiating transcription using the target promoter and bridging the promoter with other regulatory elements in the locus.ConclusionsThe widespread chained structure of gene enhancers in humans reveals that the primary, critical enhancer is distal, commonly located further away than other enhancers. This first, distal enhancer establishes contacts with multiple regulatory elements and safeguards a complex regulatory program of its target gene.

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