Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Abstract

Chromatin organization is essential for DNA packaging and gene regulation in eukaryotic genomes. While significant progresses have been made, the exact molecular arrangement of nucleosomes remains controversial. Using a well-calibrated residue-level coarse-grained model and advanced dynamics modeling techniques, particularly the non-Markovian dynamics model, we map the free energy landscape of tetra-nucleosome systems, identify both metastable conformations and intermediate states in folding pathways, and quantify the folding kinetics. Our findings show that chromatin with 10n basepair (bp) DNA linker lengths favors zigzag fibril structures. However, longer linker lengths destabilize this conformation. When the linker length is 10n+5 bp, chromatin loses the unique dominant conformation, favoring a dynamic ensemble of structures resembling folding intermediates. Embedding the tetra-nucleosome in a nucleosome condensate similarly shifts stability toward folding intermediates as a result of the competition of internucleosomal contacts. These results suggest that chromatin organization observed in vivo arises from the unfolding of fibril structures due to nucleosome crowding and linker length variation. This perspective aids in unifying experimental studies to develop molecular models for chromatin.