Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding

Abstract

Transcription factor (TF) proteins bind to DNA to regulate gene expression. Normally, accessibility to DNA is required for their function. However, in the nucleus, the DNA is often inaccessible, wrapped around histone proteins in nucleosomes forming the chromatin. Pioneer TFs are thought to induce chromatin opening by recognizing their DNA binding sites on nucleosomes. For example, Oct4, a master regulator and inducer of stem cell pluripotency, binds to DNA in nucleosomes in a sequence-specific manner. Here, we reveal the structural dynamics of nucleosomes that mediate Oct4 binding from molecular dynamics simulations. Nucleosome flexibility and the amplitude of nucleosome motions such as breathing and twisting are enhanced in nucleosomes with multiple TF binding sites. Moreover, the regions around the binding sites display higher local structural flexibility. Probing different structures of Oct4-nucleosome complexes, we show that alternative configurations in which Oct4 recognizes partial binding sites display stable TF-DNA interactions similar to those observed in complexes with free DNA and compatible with the DNA curvature and DNA-histone interactions. Therefore, we propose a structural basis for nucleosome recognition by a pioneer TF that is essential for understanding how chromatin is unraveled during cell fate conversions.

Histone tails cooperate to control the breathing of genomic nucleosomes

“…The 146 bp Widom nucleosomes with Drosophila melanogaster and Homo Sapiens histones were built by homology modelling, using Modeller (https://salilab.org/modeller/), with the same procedure described in our previous report ( 38 ). As templates, we used the structure of the Drosophila melanogaster nucleosome core (PDB ID: 2PYO), the structure of the Widom 601 nucleosome particle (PDB: 3LZ0), and the crystal structure of the X. laevis nucleosome that includes histone tails (PDB: 1KX5).…”

“…The Esrrb and Lin28b enhancer sequences were the same as used in our previous work ( 38 ) (Supplementary Document S1), originally selected from data by Soufi et al ( 45 ). We substituted the Widom sequence with the Lin28b and the Esrrb sequences using the “swapna” function in Chimera (https://www.cgl.ucsf.edu/chimera/).…”

“…In the human Lin28b nucleosome, the sequence was shifted by 1 extra bp (2 compared to the construct presented in Soufi et al (46)). This shift was introduced following our previous work (38) to optimize the accessibility of the Oct4 binding sites.…”

“…The structural flexibility of the tails was demonstrated in simulations of free histones or tail mimicking peptides (30,31). In the few atomistic simulations of complete nucleosomes reported to date, the structural flexibility was limited due to the short time scales or the small number of trajectories (32)(33)(34)(35)(36)(37)(38). For example, limited nucleosome breathing and the collapse of histone tails on DNA was observed in a few 1µs simulations (35).…”

“…For gene regulation in cells, the structural flexibility and mobility of nucleosomes with genomic DNA sequences matters most: genomic nucleosomes are more dynamic than engineered ones ( 42 ). Recently, we reported large amplitude breathing and twisting motions from MD simulations of 2 genomic nucleosomes ( 38 ), which bear enhancer sequences of the genes ESRRB and LIN28B. These genes are important for stem cell pluripotency ( 43, 44 ) and their nucleosome wrapped enhancers are bound by the key pioneer transcription factor Oct4 when converting skin to stem cells ( 45,46 ).…”