High-resolution map of chromatin accessibility - insights into the focused binding of a large number of transcription factors

TL;DR

This study maps chromatin accessibility in human cells and shows how transcription factors bind in focused regions linked to nucleosome depletion.

Contribution

A high-resolution map of chromatin accessibility and a model of TF co-binding in nucleosome-depleted regions.

Findings

Over 25,000 focused TF binding sites were identified in each cell type, linked to nucleosome depletion.

Most TFs bind to sites without their canonical motifs, suggesting cooperative binding mechanisms.

Phenotypically causal variants and functional motifs are enriched in focused binding sites.

Abstract

Emerging evidence has shown the common occupancy of dozens to hundreds of transcription factors (TFs) on cis-regulatory elements (CREs), yet the underlying details are largely unknown.

In this study, leveraging extensive collections of TF ChIP-seq data of more than 1000 TFs in human HepG2 and K562 cells, we located highly focused TF binding sites (FBSs) within CREs as single-nucleosome depleted regions, which accommodate the majority of the total TF binding events. Approximately 25,000 strong FBSs were identified in each cell type. For more than 90% of TFs, including some pioneer factors such as GATA1 and JUN, their binding sites out of FBSs barely show nucleosome depletion. Essential cellular function related motifs and phenotypically causal variants are strongly enriched in the FBSs, but not in their immediate flanking regions within CREs. Most TFs bind to FBSs not containing their canonical motifs.

Our study revealed the critical connection between highly focused TF binding and the nucleosome depleted status of DNA in vivo. Meanwhile, we constructed high-resolution maps of chromatin accessibility at distal CREs in the two human cells. We propose a model of TF co-binding in vivo and suggest that a short DNA residence time of most TFs underlies the requirement of a large number of TFs for sustained nucleosome depletion at CREs.

The online version contains supplementary material available at 10.1186/s13072-026-00665-2.

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