Hoerner, L. | bioRxiv Science

bioRxiv2026

Modular control of CpG islands by chromatin-opening transcription factors specifies transcription start sites

CpG islands (CGIs) constitute the dominant class of promoters in vertebrate genomes, yet the mechanisms underlying their transcription initiation remain unclear. Using deep learning and acute perturbation of twelve transcription factors (TFs), we show that chromatin-opening TFs are the primary determinants of initiation site selection, thereby governing promoter output. The dominant TF defines a nucleosome-free region and specifies where transcription begins by binding closest to the transcription start site. Loss of this TF redirects transcription initiation to an adjacent secondary TF position, partially buffering gene expression. Promoter variant analyses validate that this modular control of initiation is encoded in cis and programmable. This principle extends to initiation at enhancers and TATA-box promoters, where chromatin-opening TFs unmask the TATA box for focused initiation. These findings point to a common sequence grammar for transcription across promoters and enhancers, supporting a minimalist and evolvable architecture of cis-regulatory regions.

molecular biology↗

bioRxiv2024

Chromatin-dependent motif syntax defines differentiation trajectories

Transcription factors recognizing short DNA sequences within gene regulatory regions are crucial drivers of cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, NGN2 and MyoD1, which recognize ubiquitous E-box motifs yet instigate distinct cell fates--neurons and muscles, respectively. Following controlled induction in embryonic stem cells, we monitor binding across differentiation trajectories, employing an interpretable machine-learning approach integrating pre-existing DNA accessibility data. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding and predicting genome engagement with high precision. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer-factors, influenced by multi-motifs, rotational spacing, flanking sequences, and specific interaction partners, accounting for subsequent lineage divergence. Extending our methodology to other models demonstrates how such combination of opportunistic-binding and context-specific chromatin opening underpin transcription factor specificity driving differentiation trajectories.

genomics↗