Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Enhancers”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2026

MYB activity drives emergent enhancer activation and enhancer-promoter interactions in acute lymphoblastic leukemia.

Aberrant enhancer usage is a defining feature of oncogenic transcriptional reprogramming. Therapeutic strategies that disrupt enhancer-driven gene regulation may offer new treatment avenues. MYB is a key hematopoietic transcription factor that is frequently dysregulated in a broad range of cancers and plays a critical role in sustaining malignant cell states, including in aggressive leukemia subtypes such as KMT2A-rearranged leukemias. The molecular mechanisms by which it maintains oncogenic transcription remain incompletely understood. Here, we investigate the role of MYB in directing pathological enhancer activity to drive oncogene expression in leukemia. Using high-resolution Micro Capture-C, we show that upon MYB degradation, highly defined enhancer-promoter interactions at MYB binding sites are lost, correlating with the significant downregulation of target gene expression. When anchored to a gene desert region, the Myb transactivation domain (MybTA) is sufficient and necessary for the nucleation of an enhancer-like region. Critically, long-range chromatin interactions are established up to 400 kb away from where MybTA is anchored. This results in the activation of transcription from distal cryptic elements, which is reduced or abolished in the presence of point mutations that disrupt its interaction with the coactivators P300/CBP. All these results indicate that MYB activity alone is sufficient to generate an enhancer, inducing transcription through precise enhancer-promoter cross talk, and identify the MYB-P300/CBP axis as a therapeutically actionable vulnerability in enhancer-driven malignancies.

Promoter Regions, Genetic↗
PubMed2022

Enhancer and super-enhancer landscape in polycystic kidney disease.

Widespread aberrant gene expression is a pathological hallmark of polycystic kidney disease (PKD). Numerous pathogenic signaling cascades, including c-Myc, Fos, and Jun, are transactivated. However, the underlying epigenetic regulators are poorly defined. Here we show that H3K27ac, an acetylated modification of DNA packing protein histone H3 that marks active enhancers, is elevated in mouse and human samples of autosomal dominant PKD. Using comparative H3K27ac ChIP-Seq analysis, we mapped over 16000 active intronic and intergenic enhancer elements in Pkd1-mutant mouse kidneys. We found that the cystic kidney epigenetic landscape resembles that of a developing kidney, and over 90% of upregulated genes in Pkd1-mutant kidneys are co-housed with activated enhancers in the same topologically associated domains. Furthermore, we identified an evolutionarily conserved enhancer cluster downstream of the c-Myc gene and super-enhancers flanking both Jun and Fos loci in mouse and human models of autosomal dominant PKD. Deleting these regulatory elements reduced c-Myc, Jun, or Fos abundance and suppressed proliferation and 3D cyst growth of Pkd1-mutant cells. Finally, inhibiting glycolysis and glutaminolysis or activating Ppara in Pkd1-mutant cells lowerd global H3K27ac levels and its abundance on c-Myc enhancers. Thus, our work suggests that epigenetic rewiring mediates the transcriptomic dysregulation in PKD, and the regulatory elements can be targeted to slow cyst growth.

Animals↗
PubMed2026

ATRX Condensates as Candidate Organizers of Enhancer-Centered Nuclear Microenvironments in Neural Progenitors: A Hypothesis for Enhancer-Associated ATRX Function in Neural Progenitors.

Neural progenitor cells (NPCs) must preserve lineage identity while remaining responsive to developmental cues. Here, we discuss the hypothesis that ATRX condensates help organize enhancer-centered nuclear microenvironments in NPCs. ATRX has long been studied in heterochromatin maintenance, histone variant deposition, and chromatin remodeling; earlier work has also shown that ATRX can occupy euchromatic and active regulatory regions and contribute to transcriptional regulation. Recent evidence in human NPCs indicates that ATRX forms nuclear puncta with condensate-like properties, associates with neurogenic enhancer-rich regions, and incorporates regulatory factors such as CHD7 and p300. Perturbation of ATRX condensate formation is associated with changes in enhancer-associated ATRX occupancy, neural gene-expression programs, and neuroepithelial organization, suggesting a regulatory mode that may complement canonical heterochromatin-associated functions. We propose a dual-mode model in which folded domains contribute to chromatin anchoring at repressive regions, whereas intrinsically disordered regions support condensate-associated organization at active developmental enhancers. We emphasize that whether ATRX condensates activate enhancers de novo, stabilize pre-existing enhancer states, buffer transcriptional variability, or primarily organize cofactor localization remains unresolved. We also discuss limitations of the current evidence and outline acute, locus-specific experiments needed to test the model.

X-linked Nuclear Protein↗
PubMed2026

Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models.

MOTIVATION: Gene expression plays a crucial role in cell function, and enhancers can regulate gene expression precisely. Therefore, accurate prediction of enhancers is particularly critical. However, existing prediction methods have low accuracy or rely on fixed multiple epigenetic signals, which may not always be available. RESULTS: We propose a two-stage framework that accurately predicts enhancers by flexibly combining multiple epigenetic signals. In the first stage, we designed a Blending-KAN model, which integrates the results of various base classifiers and employs Kolmogorov-Arnold Networks (KAN) as a meta-classifier to predict enhancers based on flexible combinations of multiple epigenetic signals. In the second stage, we developed a Stacking-Auto model, which extracted sequence features using DNABERT-2 and located the enhancers based on the Stacking strategy and AutoGluon framework. The accuracy of the Blending-KAN model reached 99.69 ± 0.11% when five epigenetic signals were used. In cross-cell line prediction, the accuracy was more significant than or equal to 93.72%. With Gaussian noise, it still maintains an accuracy of 98.74 ± 0.03%. In the second stage, the accuracy of the Stacking-Auto model is 80.50%, which is better than the existing 17 methods. The results show that our models can be flexibly used to predict and locate enhancers utilizing a combination of multiple epigenetic signals. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/emanlee/Hi-Enhancer and https://doi.org/10.6084/m9.figshare.29262158.v1.

Enhancer Elements, Genetic↗
PubMed1975

An extravascular component of contrast enhancement in cranial computed tomography. Part II. Contrast enhancement and the blood-tissue barrier.

The authors provide evidence of significant extravasation of contrast media responsible for the contrast enhancement of pathological tissue on computed tomography. The tissue-blood ratio of enhancement was calculated by the EMI scanner in 2 patients after injection of contrast material and prior to surgery; tumor-blood ratios for red blood cell and plasma tracers were calculated after surgery. The ratios of enhancement demonstrated the analogy between contrast enhancement and the leaking of radionuclide across the blood-brain barrier. This phenomenon may cause error if this technique is used for the measurement of cerebral blood volume. The area for complementary roles of CT and radionuclide brain imaging seems to be narrower than expected.

Animals↗
PubMed1975

Immunologic enhancement of rat renal allografts. III. Immunopathologic lesions and rejection in long-surviving passively enhanced grafts.

Immunologic enhancement of renal allografts from (Lewis times Brown Norway) F1 to Lewis rats was achieved by administering a single dose of antidonor serum at the time of transplantation. A series of grafts functioning for 1 to 4 months after transplantation were examined by light and immunofluorescence microscopy to evaluate the long-term protective effects of the enhancing serum and to determine if previously unobserved lesions appeared in long survivors. Despite the absence of detectable circulating cytotoxic alloantibody, long-term allografts showed necrotizing glomerular and arterial lesions which resembled those seen in acutely rejecting grafts and were compatible with humoral rejection. Thus, in this model, there is a late decline in the ability of passive enhancement to inhibit humoral rejection. Long-term grafts also developed tubular lesions with deposition of immunoglobulin and complement on the tubular basement membranes (TBM). Anti-TBM antibodies were demonstrated in recipients' sera and found to be organ specific but not major histocompatibility antigen or species specific. This tubular lesion is therefore a unique form of allograft injury in which the immune response is directed against tissue antigen(s) which are distinct from the major histocompatibility antigens that induce rejection.

Animals↗
PubMed1977

Enhancement of 5-iododeoxyuridine-induced endogenous C-type virus activation by polycyclic hydrocarbons: apparent lack of parallelism between enhancement and carcinogenicity.

When mouse MLg cells were treated with 3-methylcholanthrene or 7,12-dimethylbenz[alpha]anthracene in the presence of microsomal enzymes and NADPH after 5-iododeoxyuridine (IUDR) treatment, the induction rate of the endogenous C-type virus was increased fivefold to sixfold in comparison with the culture treated with IUDR only. In this reaction, both the microsomal enzymes and NADPH were indispensable. 7,8-Benzoflavone, an inhibitor of the metabolism of hydrocarbons in hamster embryo cultures, inhibited the reaction. For detecting the enhancing activity, the concentration of IUDR for the pretreatment, the concentration of the test products, and the duration of the treatment with the products were important factors. In screening 30 polycyclic hydrocarbons, we were unable to detect a correlation between the in vivo carcinogenicity in the skin and the enhancing activity in the conditions tested.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1975

An extravascular component of contrast enhancement in cranial computed tomography. Part I. The tissue-blood ratio of contrast enhancement.

One can calculate the tissue-blood ratio of enhancement by analyzing the quantitative aspects of the CT scans of the cranium and blood samples both before and after the injection of contrast medium. This ratio is equivalent to that between the iodine content of a given volume of tissue and an equal volume of blood. Analysis of 47 normal patients, including 27 with pathological brain lesions, indicated that there is significant extravasation of contrast medium in patients with such lesions.

Brain↗
PubMed2025

H3K4me2 marks the enhancer: Enhancer logic in the zebrafish embryo.

At a key point in development, the embryo activates its genome: a shift that is largely coordinated by maternally derived factors. A new study in PLOS Biology identifies H3K4me2-marked enhancers in zebrafish that function independently and mirror the gamete state.

Animals↗
PubMed2026

Enhancement flavor quality in Zhao'an Baxian oolong tea through enhanced turning-over process.

A systematical investigation on the effects of turning-over intensity on the flavor formation of Zhao'an Baxian oolong tea (ZBT) was performed, through a comparative analysis of heavy turning-over (HT) and light turning-over (LT) treatments in this study. The tea samples were subjected to proteomic and metabolomic analyses, combined with quantitative descriptive analysis (QDA) and electronic sensory (E-tongue/E-nose) evaluation. The results demonstrate that HT significantly reduced the content of bitter and astringent compounds, such as catechins and flavonol glycosides, while promoting the accumulation of umami-related amino acids. Concurrently, HT enhanced the biosynthesis of key floral and fruity volatiles, such as β-ocimene, geraniol, benzaldehyde, jasmone by activating stress-responsive metabolic pathways. These coordinated biochemical changes, driven by enzyme-catalyzed reactions in response to prolonged mechanical wounding and environmental stress, collectively improved the overall sensory profile of ZBT. These findings provide a mechanistic foundation for improving ZBT production, with clear implications for quality control and flavor-oriented product development.

Tea↗
PubMed1975

[Spleen enhancement reactions in chick embryo after homografting adult chicken spleen fragments: changes in spleen cell population in relation to rate of spleen enhancement].

A method using the comparison between the modifications of spleen weight and on spleen smears visible modifications of the distribution into categories of cells which are classified by the mean of their maturation degree, suggested that these both types of modifications are bound. Therefore, the classic cytological study seems to be a really good tool for analysing the effects of this kind of grafting on the haemopoietic organs, the weight modifications of which are difficult to measure. On the other hand, this method allowed us to see that the distribution of the cell population in the weakly enlarged spleens is very different from both distribution of the population in the strongly enlarged spleens and the controls ones ; this heterogeneity of the stimulating effect of the graft asked us the question whether this one could exerce its influence by the mean of two different ways, at least, or by only one.

Animals↗
PubMed1976

Organization of monkey superior colliculus: enhanced visual response of superficial layer cells.

1. Cells in the superficial layers of monkey superior colliculus respond more vigorously to a spot of light falling in their receptive fields when the monkey uses that spot of light as the target for a saccadic eye movement. Our purpose in these experiments was to investigate the characteristics of this enhancement effect. While monkeys fixated, we determined the response of a cell to a stimulus falling in its receptive field. Then we determined the response of the cell to the same stimulus when the monkey made a saccade to the stimulus or near to it. 2. The enhancement of the visual response is spatially limited. The receptive field of a cell always shows enhancement throughout its extent and frequently shows a slight expansion. Saccades made near to a stimulus in the visual receptive field, but not to it, also lead to an enhancement of that visual stimulus; an area around the excitatory center of the receptive field where such enhancement occurs was referred to as the enhancement field of the cell. An enhanced response in one part of the visual field was not accompanied by depressed responses associated with saccades to other parts of the visual field. 3. The enhancement effect is temporally limited; it begins 200-300 ms before the eye movement, as determined by the increasing response to 50-ms light pulses presented at varying intervals before the eye movement. The degree of enhancement intensifies when the visual stimulus is turned on closer in time to the onset of the saccade. A buildup of the enhancement also occurs on successive trials as does the response of eye movement-related cells in the intermediate layers. 4. The enhancement response is not present in the upper quarter-millimeter of the superficial layers, suggesting that the effect is not present in retinal afferents which terminate primarily in this area of the superficial layers. The enhancement effect is seen throughout the visual field; the foveal area was not tested. 5. In order to determine the relation of the enhancement effect to the monkey's behavioral response, we required the monkey to make a hand response rather than an eye movement-response to the visual stimuli. Cells did not show a clear enhancement with such a hand response. Results of these experiments indicate that the enhancement effect is dependent on the type of response the monkey makes to the stimulus and is probably specifically related to eye movements. Since the enhancement of visual response seems likely to be related specifically to eye movements both on physiological and behavioral grounds, the response-free term "attention" is probably inappropriate for the phenomenon. 6. The hypothesis advanced in the preceding paper that eye movement-related activity from intermediate and deep colliculus layers is directed upward to converge with visually related activity in the superficial layers is extended to include an input from cells in these deeper layers (or their afferents) to the superficial layer cells...

Animals↗
PubMed2025

dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data.

MOTIVATION: scATAC-seq enables high-resolution mapping of cis-regulatory elements. It has been widely applied to uncover cell-type-specific regulatory networks and complement scRNA-seq analysis in numerous studies. However, a large number of datasets generated by scATAC-seq remain underutilized due to limited exploration of super-enhancers/typical enhancers and gene markers. A comprehensive resource enabling cell-type-specific annotation of cis-regulatory elements and their dynamic enhancer-gene linkages remains an urgent unmet need for scATAC-seq. RESULTS: We present dbscATAC, a specialized single-cell database for annotating super-enhancers, gene markers, and enhancer-gene interactions derived from scATAC-seq data. Using improved machine learning algorithms, we identified 213 835 super-enhancers across 520 tissue/cell types from three species, as well as 347 484 gene markers, 13 470 526 enhancers, and 10 402 346 enhancer-gene interactions derived from 1 668 076 single cells spanning 1028 tissue/cell types in 13 species. An easy-to-use online platform with multiple analytic modules and hierarchical query options was developed for searching, browsing and visualizing single-cell super-enhancers, enhancers, and gene markers. dbscATAC provides a comprehensive resource to facilitate the exploration of enhancer landscapes, gene regulation, and cell-type-specific characteristics in single-cell epigenomics. AVAILABILITY AND IMPLEMENTATION: The database with all the super-enhancer/enhancer annotation data is available at http://singlecelldb.com/dbscATAC/index.php. And the source code of dbscATAC for prediction of SEs, enhancers, and gene markers are available at https://github.com/EvansGao/dbscATAC. The source code, tissue/cell type description, and data summary can be downloaded at DOI: 10.6084/m9.figshare.28706414.scATAC-seq, Database, Super-enhancers/enhancers, Gene markers.

Enhancer Elements, Genetic↗
PubMed2026

An encyclopedia of human enhancer-gene regulatory interactions.

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the effect of human genetic variation on disease1-6. Here we create and evaluate a resource of more than 92 million enhancer-gene regulatory interactions across 1,458 biosamples covering 369 cell types and tissues, by integrating predictive models, chromatin states, three-dimensional contacts and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,356 element-gene pairs measured in CRISPR perturbation experiments, more than 30,000 fine-mapped expression quantitative trait loci and 569 fine-mapped genome-wide association study (GWAS) variants linked to a probable causal gene. Using this framework, we develop ENCODE-rE2G, a predictive model achieving state-of-the-art performance across several prediction tasks, demonstrating that iterative perturbations and supervised machine learning can build increasingly accurate predictive models of enhancer regulation. Using ENCODE-rE2G, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes and improving analyses linking noncoding variants to target genes and cell types for common complex diseases. By interpreting the model, we find that beyond enhancer activity and three-dimensional enhancer-promoter contacts, additional features that guide enhancer-promoter communication include promoter class and enhancer-enhancer synergy. These genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

Humans↗