Enhancer Promoter Interaction

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A curated benchmark of enhancer-gene interactions for ...

(6 days ago) Jan 22, 2020 · First, gene expression may be a better readout for enhancer-gene interactions than a promoter’s chromatin accessibility, although these two features are correlated (average Pearson correlation r = 0.68). Second, for the DNase-expression method, Sheffield et al. generated normalized, batch-corrected matrices for the DNase-seq and gene ...

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1924-8

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Enhancer Interaction Networks as a Means for Singular ...

(4 days ago) Oct 23, 2014 · Thus, enhancer interactions in trans may be favored by—but are not a simple product of—the convergence of linked ORs, a result that is consistent with the observation that Bptf deletion impairs enhancer interactions, but not OR aggregation. Download : Download high-res image (563KB) Download : Download full-size image; Figure 7.

https://www.sciencedirect.com/science/article/pii/S0092867414011829

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Disruption of OTC promoter-enhancer interaction in a ...

(3 days ago) (ii) The promoter variation c.-366A>G does not affect the function of the promoter alone but it disrupts the interaction of the promoter with the enhancer. (iii) The promoter-enhancer interaction contributes to tissue specific expression of OTC in the liver. We conclude that mutations in the regulatory regions of OTC can lead to OTCD and should ...

https://pubmed.ncbi.nlm.nih.gov/20127982/

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Robust Hi-C Maps of Enhancer-Promoter Interactions …

(7 days ago) Aug 06, 2020 · Insulators (with CTCF), promoters (with H3K4me3), and enhancers (with H3K27ac) are clearly top contributors to chromatin loops (Figure 4C). Interestingly, the numbers of enhancer or promoter interactions increased in hNPCs and hNeurons more than in hiPSCs (Figure 4C).

https://www.sciencedirect.com/science/article/pii/S1097276520303920

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Mechanisms of Enhancer-Promoter Interactions in Higher ...

(5 days ago) Jan 12, 2021 · The interaction between an enhancer and a promoter can be stabilized by CCCTC-binding factor (CTCF), in cooperation with the cohesin complex and the dimerization of LOB domain-containing protein 1 (LDB1), which is recruited to chromatin through interactions with LIM proteins.

https://www.mdpi.com/1422-0067/22/2/671/htm

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Enhancer–promoter interactions and transcription | …

(3 days ago) May 06, 2020 · Enhancer–promoter interactions and transcription. A new study addresses whether transcription of enhancers and the resulting enhancer RNAs (eRNAs) play a …

https://www.nature.com/articles/s41588-020-0620-7

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Long-range enhancer–promoter contacts in gene …

(7 days ago) May 13, 2019 · Along with studies profiling promoter interactions at high resolution during cellular differentiation 19,20,21,22, these studies support the notion that modulating the frequency of enhancer ...

https://www.nature.com/articles/s41576-019-0128-0

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Mapping enhancer and promoter interactions

(6 days ago) Mar 27, 2012 · The remaining 478 interactions were reported to be enhancer-enhancer interactions. A global analysis of the interactions found that 9% of enhancers with long-range interactions interact with multiple promoters and 25% of interacting promoters have more than one …

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343664/

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Risk SNP-Mediated Enhancer-Promoter Interaction Drives ...

(8 days ago) Risk SNP-Mediated Enhancer-Promoter Interaction Drives Colorectal Cancer through Both FADS2 and AP002754.2. Cancer Res. 2020 May 1;80(9):1804-1818. doi: 10.1158/0008-5472.CAN-19-2389. Epub 2020 Mar 3. Authors Jianbo ...

https://pubmed.ncbi.nlm.nih.gov/32127356/

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Enhancer-promoter interactions are encoded by complex ...

(7 days ago) The resulting models accurately predict individual enhancer-promoter interactions across multiple cell lines with a false discovery rate up to 15 times smaller than that obtained using the closest gene. By evaluating the genomic features driving this accuracy, we uncover interactions between structural proteins, transcription factors ...

https://pubmed.ncbi.nlm.nih.gov/27064255/

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An intriguing characteristic of enhancer-promoter interactions

(5 days ago) Mar 08, 2021 · Enhancers are short genomic regions that can boost the condition-specific transcription of their target genes [1, 2].They directly interact with the promoters of their target genes via chromatin looping to control the temporal and spatial expression of target genes [3–7].Enhancers can be several dozens to a couple of thousand base pairs (bps) long and can be located in the distal upstream or ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07440-5

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FOCS predicted enhancer-promoter interactions - TAU

(3 days ago) Enhancer/Promoter regions were resized to 100/200 bp, respectively. Please refer to the 'FOCS predicted enhancer-promoter interactions' table below for the original sizes. Human (hg19) FOCS predictions. Mouse (mm9) FOCS predictions on FANTOM5 data.

http://acgt.cs.tau.ac.il/focs/download.html

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EPIP: a novel approach for condition-specific enhancer ...

(6 days ago) Oct 15, 2019 · EPIP stands for ‘Enhancer–Promoter Interaction Prediction’. It is a supervised learning-based approach that utilizes functional genomic and epigenomic data to build a robust model to predict shared and condition-specific EPIs. EPIP can work with missing data, different types of datasets and even a dataset with a partial list of features. ...

https://academic.oup.com/bioinformatics/article-abstract/35/20/3877/5549495

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In the loop: promoter–enhancer interactions and bioinformatics

(3 days ago) Nov 19, 2015 · Enhancer–promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter–enhancer interactions (PEIs).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142009/

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Transcription factors mediate long-range enhancer–promoter ...

(8 days ago) Dec 01, 2009 · DNA Looping Mediates the Interaction Between a Remote Enhancer and a Promoter. To test whether enhancer–promoter communication involves contacts between the distant regulatory elements, we carried out chromosome conformation capture (3C) assays in which enhancer DNA sequences are ligated to promoter DNA sequences only if they are in close physical proximity.

https://www.pnas.org/content/106/48/20222

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EPIsHilbert: Prediction of Enhancer-Promoter Interactions ...

(8 days ago) Jul 19, 2021 · Enhancer-promoter interactions (EPIs) play a significant role in the regulation of gene transcription. However, enhancers may not necessarily interact with the closest promoters, but with distant promoters via chromatin looping. Considering the spatial position relationship between enhancers and their target promoters is important for predicting EPIs.

https://www.mdpi.com/2073-4425/12/9/1385/htm

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Global view of enhancer–promoter interactome in human ...

(7 days ago) May 27, 2014 · Feature 1: Enhancer and target promoter activity profile correlation (EPC). Recently, Ernst et al. have shown that correlation between enhancer and promoter histone modification patterns can be used to infer their interactions.We extended this approach and asked whether there is a correlation in the activities of enhancers and promoters across multiple cell types.

https://www.pnas.org/content/111/21/E2191

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Prediction of enhancer-promoter interactions via natural ...

(3 days ago) May 09, 2018 · Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting ones since the power of traditional experimental methods is limited due to low ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4459-6

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Risk SNP-Mediated Enhancer–Promoter Interaction Drives ...

(7 days ago) May 01, 2020 · In the present study, we found that there have significant interactions between rs174575-enhancer region and the promoter regions of both FADS2 and AP002754.2 in an allele-specific manner, suggesting that the risk allele of rs174575 can facilitate long-range enhancer–promoter interactions to promote FADS2 and AP002754.2 expression.

https://cancerres.aacrjournals.org/content/80/9/1804

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Exploiting XG Boost for Predicting Enhancer-promoter ...

(5 days ago) Title:Exploiting XG Boost for Predicting Enhancer-promoter Interactions VOLUME: 15 ISSUE: 9 Author(s):Xiaojuan Yu, Jianguo Zhou, Mingming Zhao , Chao Yi, Qing Duan*, Wei Zhou* and Jin Li* Affiliation:Software School of Yunnan University, Kunming, Software School of Yunnan University, Kunming, Software School of Yunnan University, Kunming, Software School of Yunnan University, …

https://www.eurekaselect.com/178425/article

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HACER - Active Enhancer Database

(5 days ago) HACER is an atlas of Human ACtive Enhancer to interpret Regulatory variants, which includes active, transcribed enhancers derived from GRO-seq, PRO-seq and CAGE data.. HACER not only contains cell-type-specific enhancers but also connects enhancers into transcriptional regulatory network by integrating TF-enhancer bindings and validated chromation interactions.

http://bioinfo.vanderbilt.edu/AE/HACER/

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Nonlinear control of transcription through enhancer ...

(3 days ago) Apr 22, 2021 · Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs)[1][1]–[4][2]. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. To address this …

https://www.biorxiv.org/content/10.1101/2021.04.22.440891v1

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CTCF-Mediated Enhancer-Promoter Interaction Is a Critical ...

(5 days ago) To investigate whether CTCF-mediated long-range enhancer-promoter interaction plays a role in controlling gene expression noise, we first analyzed genome-wide chromatin interactions of mouse Th2 cells using a three-enzyme Hi-C protocol (3e Hi-C) that cleaves chromatin with a pool of three 4 bp-restriction enzymes (see STAR Methods for details, Figures S1A–S1C and Table S1).

https://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30624-X

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Enhancer (genetics) - Wikipedia

(7 days ago) In genetics, an enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors.Enhancers are cis-acting.They can be located up to 1 Mbp (1,000,000 bp) away from the gene, upstream or downstream from the start site.

https://en.wikipedia.org/wiki/Enhancer_(genetics)

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Predict long-range enhancer regulation based on protein ...

(5 days ago) This enhancer–promoter interaction, which only shows an activity correlation of 0.261, is successfully predicted based on the PPI between enhancer-binding CTCF and promoter-binding ELF1. Overall, these results demonstrate that TF PPI features can improve the delineation of specific interacting enhancer–promoter pairs from neighboring non ...

https://academic.oup.com/nar/article/49/18/10347/6376026

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Predicting stimulation-dependent enhancer-promoter ...

(8 days ago) Sep 28, 2017 · We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with …

https://peerj.com/articles/3742/

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EPnet: A general network to predict enhancer-promoter ...

(7 days ago) May 23, 2021 · The mechanism of spatio-temporal gene expression is significantly related to the interaction between the two regulatory elements on the DNA, enhancer and promoter. Identifying enhancer-promoter interactions that disrupt cell-specific gene expression and cause different human diseases remains to be a great challenge. To figure this out, we construct a sequence-based deep …

https://ieeexplore.ieee.org/document/9440647

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The first enhancer in an enhancer chain safeguards ...

(6 days ago) Sep 12, 2019 · The primary promoter-enhancer contact is commonly established by a distal enhancer. We constructed regulatory element networks of interactions among regulatory elements in GM12878, HMEC, HUVEC, and K562 cell lines [].Similar to the ribonucleic acid polymerase II (RNAPII)-associated chromatin interaction network [], all enhancers and promoters were denoted as vertices, while the …

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1808-y

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What is the Difference Between Enhancer and Promoter ...

(8 days ago) Oct 02, 2018 · Through the location is far away from the promoter, enhancers are spatially close to the promoter, allowing the interactions with RNA polymerase and basal transcription factors. The activators bound to the enhancer region then bind with a mediator complex, which in turn recruit the RNA polymerase and the basal transcription factors to the ...

https://pediaa.com/what-is-the-difference-between-enhancer-and-promoter/

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EPnet: A general network to predict enhancer-promoter ...

(3 days ago) Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive.

https://www.researchgate.net/publication/352122957_EPnet_A_general_network_to_predict_enhancer-promoter_interactions

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Enhancer and promoter interactions — long distance calls ...

(6 days ago) In some cases, enhancer-promoter interaction appears to be directly facilitated by CTCF/cohesin occupancy. In other cases, the promoter or the enhancer is occupied by CTCF/cohesin and additional factors cooperate to support interaction between them. It will be important to determine the exact geometry of the CTCF/cohesin binding sites vis-à ...

http://europepmc.org/articles/PMC3342482

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Predicting enhancer-promoter interaction from genomic ...

(4 days ago)

https://link.springer.com/article/10.1007/s40484-019-0154-0

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Chromatin Loops as Allosteric Modulators of Enhancer ...

(6 days ago) Oct 23, 2014 · Author Summary In eukaryotes, enhancers directly contact promoters over large genomic distances to regulate gene expression. Characterizing the principles underlying these long-range enhancer-promoter contacts is crucial for a full understanding of gene expression. Recent experimental mapping of chromosomal interactions by the Hi-C method shows an intricate network of local looping ...

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003867

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CRISPR Inversion of CTCF Sites Alters Genome Topology and ...

(7 days ago) Aug 13, 2015 · A key observation, relevant to the present study, was that the CBSs in the Pcdh HS5-1 enhancers downstream of the α cluster and in each of the promoters and downstream exons are configured in opposite orientations (Guo et al., 2012).Chromosome Conformation Capture (3C) studies revealed that CTCF/cohesin-mediated DNA looping occurs exclusively between paired CBSs within …

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642453/

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Local epigenomic state cannot discriminate interacting and ...

(3 days ago) Dec 18, 2018 · a) For cell line K562, and b) for cell line GM12878, for each promoter we show the number of positive and negative EP pairs sharing a promoter. In a) for example, there are 27 interactions in position (7,2), which means three distinct promoters each interact positively with 7 enhancers and negatively with two enhancers in the training data. When the number of negative and …

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625

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ENC EPD Enhc-Gene Track Settings

(3 days ago) EPDnew mouse promoter release 003 (June 2018) was obtained from obtained from the Eukaryotic Promoter Database, and filtered to contain only promoters appearing in the Enhancer/Gene maps. The Interactions view was generated at UCSC from the Enhancer/Gene maps by linking the enhancers to promoter regions based on the EPDnew promoters.

https://genome-asia.ucsc.edu/cgi-bin/hgTrackUi?db=mm10&c=chrX&g=encode3RenEnhancerEpdNewPromoter

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Chromosome conformation capture - Wikipedia

(6 days ago) Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, [4] or they may be converted to distances and used to reconstruct 3-D structures.

https://en.wikipedia.org/wiki/Chromosome_conformation_capture

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Enhancer-promoter interactions are encoded by complex ...

(9 days ago) Enhancer-promoter interactions (EPIs) play a significant role in the regulation of gene transcription. However, enhancers may not necessarily interact with the closest promoters, but with distant ...

https://www.researchgate.net/publication/301217500_Enhancer-promoter_interactions_are_encoded_by_complex_genomic_signatures_on_looping_chromatin

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