Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancer-promoter interactions in acheiropodia patient's cells

ABSTRACT: Enhancer-promoter interactions in acheiropodia patient's cells

PROVIDER: PRJNA649358 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12341917.fastq.gz	Fastqsanger.gz
	SRR12341918.fastq.gz	Fastqsanger.gz
	SRR12341919.fastq.gz	Fastqsanger.gz
	SRR12341920.fastq.gz	Fastqsanger.gz
	SRR12341921.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Enhancer-promoter interactions in acheiropodia patient's cells

Project description:Acheiropodia, congenital limb truncation, is associated with homozygous deletions in the LMBR1 gene around ZRS, an enhancer regulating SHH during limb development. How these deletions leads to this phenotype is unknown. Using whole-genome sequencing, we fine-mapped the acheiropodia-associated region to 12 kb and show that it does not function as an enhancer. CTCF and RAD21 ChIP-seq together with 4C-seq and DNA FISH identify three CTCF sites within the acheiropodia-deleted region that mediate the interaction between the ZRS and the SHH promoter. This interaction is substituted with other CTCF sites centromeric to the ZRS in the disease state. Mouse knockouts of the orthologous 12 kb sequence have no apparent abnormalities, showcasing the challenges in modelling CTCF alterations in animal models due to inherent motif differences between species. Our results show that alterations in CTCF motifs can lead to a Mendelian condition due to altered enhancer-promoter interactions.

2020-07-30 | GSE155324 | GEO

Analysis of enhancer-promoter connectivity alterations

Project description:The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization

| EGAS00001007411 | EGA

The Mediator complex regulates enhancer-promoter interactions

Project description:The Mediator complex regulates enhancer-promoter interactions

| PRJNA848747 | ENA

Genome-wide mapping of promoter-enhancer interactions with HiCap [HiCap]

Project description:Although the locations of promoters and enhancers have been identified in several cell types, we have yet limited information on their connectivity. We developed HiCap, which combines Hi-C with promoter sequence capture, to enable genome-wide identification of regulatory interactions with single-enhancer resolution. HiCap analyses of mouse embryonic stem cells (mESC) identified promoter-enhancer interactions predictive of gene expression change upon perturbation, opening up for genomic analyses of long-range gene regulation. HiCap was designed by combining Hi-C with with sequence capture (for all promoters) and carried out in mouse embryonic stem cells (mESC)

2015-07-06 | E-GEOD-60494 | biostudies-arrayexpress

Genome-wide mapping of promoter-enhancer interactions with HiCap [RNA-seq]

2015-07-06 | E-GEOD-60493 | biostudies-arrayexpress

Transcriptional binding patterns involved in promoter-enhancer interactions.

Project description:Transcriptional binding patterns involved in promoter-enhancer interactions.

| PRJEB11488 | ENA

Nonlinear control of transcription through promoter-enhancer interactions

Project description:Nonlinear control of transcription through promoter-enhancer interactions

| PRJNA722525 | ENA

Increased Enhancer—Promoter Interactions during Developmental Enhancer Activation in Mammals

Project description:Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, we investigate the 3D conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. 61% of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer–promoter and enhancer–enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer–promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general significance of enhancer–promoter physical proximity for developmental gene activation in mammals.

2024-01-03 | GSE217078 | GEO

Transcriptional binding patterns involved in promoter-enhancer interactions.

Project description:This study was designed to be able to determine the interactions between promoter and enhancer elements in the haematopoietic stem/progenitor cell line HPC-7. The next step was to investigate if specific transcription factors could be associated with looping events and to determine if there was co-operative binding involved.

2016-02-29 | E-MTAB-3954 | biostudies-arrayexpress

The Mediator complex regulates enhancer-promoter interactions [Cut&Tag]

Project description:The Mediator complex regulates enhancer-promoter interactions [Cut&Tag]

| PRJNA848214 | ENA