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

ABSTRACT: Alternative DNA conformation formed by sequences called flipons are thought to play an important role in regulating various genomic processes, either repressing or enhancing transcription, chromatin organization, DNA repair, telomere maintenance, RNA splicing, translation, and stress responses. The formation of G-quadruplexes (GQs) has been investigated experimentally using various methodologies with varying degrees of overlap between the results underscoring the need for a gold-standard GQ dataset. With this aim we trained a large language model, GQ-DNABERT using EndoQuad, the most comprehensive human GQ dataset. GQ-DNABERT recalled the training data and predicted de novo GQs in intergenic and intronic regions, enriched for cis-regulatory elements (cCREs) and ATAC-seq peaks. We evaluated

SUBMITTER: Konovalov D 

PROVIDER: S-EPMC12526042 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature