Abstract
During cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation. Here, we use high-resolution nucleosome mapping in human cells to explore the impact of the position of GATA motifs on the surface of nucleosomes on productive enhancer formation, finding productivity correlates with binding sites located near the nucleosomal dyad axis. Biochemical experiments with model nucleosomes demonstrate sufficiently stable transcription factor-nucleosome interaction to empower cryo-electron microscopy structure determination of the complex at 3.15 Å resolution. The GATA3 zinc fingers efficiently bind their target 5′-GAT-3′ sequences in the nucleosome when they are located in solvent accessible, consecutive major grooves without significant changes in nucleosome structure. Analysis of genomic loci bound by GATA3 during reprogramming suggests a correlation of recognition motif sequence and spacing that may distinguish productivity of new enhancer formation.
Highlights
During cellular reprogramming, the pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation
Elegant structural studies of the GATA3 zinc fingers complexed with its target DNA revealed that the two zinc fingers bind to two neighboring 5′-GAT-3′ sequences located within the same major groove of the DNA15
We considered 5′-GAT-3′ tandem sequences located on the same strand as well as sequences in which 5′-GAT-3′ were located on different DNA strands in a 200 bp window centered on the center of the ChIP-seq peak
Summary
The pioneer transcription factor GATA3 binds chromatin, and in a context-dependent manner directs local chromatin remodeling and enhancer formation. GATA3 functions to establish new cell fates in cellular reprogramming systems[6,7,8] including driving of a mesenchymal to epithelial transition in breast cancer cell lines[9,10]. In these processes, GATA3 is proposed to bind target DNA sequence wrapped tightly within a positioned nucleosome and to induce chromatin remodeling, probably by recruiting a nucleosome remodeler[11]. In the most abundant category of loci identified (termed G2), GATA3 bound to transposase-accessible
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