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The delicate interplay between chromatin binding proteins and the nucleosome core particle orchestrates fundamental cellular processes. While the 147 bp DNA wrapped around four pairs of highly conserved core histones presents a seemingly symmetrical stage, we find a captivating asymmetry in protein binding affinities tunable by the DNA sequence on each side. Using atomistic molecular dynamics simulations and meticulous structural analyses, we unveil that chromatin factors Sir3, PRC1, RCC1, and
SAGA-DUB prefer the nucleosomal gyre that binds DNA more strongly also. However, another factor, known as 53BP1 prefers the gyre with the weaker DNA binding affinity. We speculate that some chromatin interactors can sense the affinity of the nucleosome's core octamer to DNA to achieve specific functional and DNA-templated outcomes such as transcription, replication or repair.
Keywords—chromatin, nucleosome, molecular dynamics, computational biophysics