Article

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication

2024-12-11

Abstract excerpt

Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While sequence-based deep learning models show promise in predicting enhancer-driven gene expression, experimental validation and human-interpretable mechanistic insights lag behind. Here, we present EXTRA-seq , a novel EXT en...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 8e9c4d47-349d-5560-8b8b-e75af4647a30
DOI: 10.1101/2024.12.08.627402

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communicationDOI 10.1101/2024.12.08.627402Read

Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wideSemantic proximity Read

Massively parallel reporter assay–informed modeling improves prediction of context-specific enhancer–gene regulatory interactionsSemantic proximity Read

EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networksSemantic proximity Read

Transcription imparts architecture, function, and logic to enhancer unitsSemantic proximity Read

An encyclopedia of enhancer-gene regulatory interactions in the human genomeSemantic proximity Read

An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patternsSemantic proximity Read

EnhancerDetector: Enhancer Discovery from Human to Fly via Interpretable Deep LearningSemantic proximity Read

Billion-Scale Deciphering of Human Gene Regulatory GrammarSemantic proximity Read

Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural NetworksSemantic proximity Read

Evolutionary conditioning enables guided generation of functionally diverse enhancersSemantic proximity Read

Effective gene expression prediction from sequence by integrating long-range interactionsSemantic proximity Read

DeepCAPE: a deep convolutional neural network for the accurate prediction of enhancersSemantic proximity Read