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October 17, 2025Nucleic Acids ResearchOpen Access

GQ-DNABERT reveals GQ proximal enhancer–promoter interactions associated with tissue-specific transcription

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Authors

DKDmitry A. KonovalovDUDmitriy UmerenkovAHAlan Herbert

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Overview

Large language model GQ-DNABERT identifies enhancer-promoter interactions in normal and cancer cells, suggesting roles in transcription regulation.

Key Points

  • GQ-DNABERT predicted enhancer-promoter pairs linked to gene expression in various tissues, enhancing transcriptional studies.
  • Notably, GQ-DNABERT's predictions were validated using extensive datasets like ENCODE and scRNA-seq, indicating strong correlations.
  • The study highlights how G-quadruplexes can serve as tissue-specific switches, affecting transcription in cancer versus normal cells.
  • Using GQ-DNABERT, researchers can extend their understanding of genomic processes and improve analyses of single-cell transcription.

Cite This Study

Konovalov et al. (2025) studied this question.

synapsesocial.com/papers/68f199d1de32064e504dd6c3https://doi.org/10.1093/nar/gkaf1007
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Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

  1. 1Analysis of live cell data with G-DNABERT supports a role for G-quadruplexes in chromatin looping2024 · 2 citations
  2. 2A Compendium of G-flipon Biological Functions that have Experimental Validation2024
  3. 3iDualG4: A Dual-Channel Deep Learning Framework for Predicting In Vivo G-Quadruplexes2026
  4. 4Multilevel ensemble for genome-wide prediction of cell-specific G-quadruplexes utilizing transformed sequences and enhanced chromatin accessibility with G4Beacon22026
  5. 5G‑quadruplexes as regulatory platforms for human transcription factors: insights from ChIP-seq data2026