Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
International journal of molecular sciences
Dec 2, 2024
Enhancers are short genomic segments located in non-coding regions of the genome that play a critical role in regulating the expression of target genes. Despite their importance in transcriptional regulation, effective methods for classifying enhance...
Enhancers are vital elements in the genome that boost the transcriptional activity of neighboring genes and are essential in regulating cell-specific gene expression. Therefore, accurately identifying and characterizing enhancers is essential for com...
Interdisciplinary sciences, computational life sciences
Nov 15, 2024
Enhancer-promoter interactions (EPIs) are crucial in gene transcription regulation and cell differentiation. Traditional biological experiments are costly and time-consuming, motivating the development of computational prediction methods. However, ex...
Although bioinformatics-based methods accurately identify SEs (Super-enhancers), the results depend on feature design. It is foundational to representing biological sequences and automatically extracting their key features for improving SE identifica...
International journal of molecular sciences
Nov 1, 2024
Enhancers are cis-regulatory DNA sequences that are widely distributed throughout the genome. They can precisely regulate the expression of target genes. Since the features of enhancer segments are difficult to detect, we propose DeepDualEnhancer, a ...
Dysregulated super-enhancer (SE) results in aberrant transcription that drives cancer initiation and progression. SEs have been demonstrated as novel promising diagnostic/prognostic biomarkers and therapeutic targets across multiple human cancers. He...
BACKGROUND: Recognition of enhancer-promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating transcription. However, experimental approaches for classifying EPIs are too expensive in terms of eff...
Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually chang...
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. It has been a long-standing goal in the field to decode the regulatory logic of an enhan...
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