Regulation of the nucleosome unwrapping rate controls DNA accessibility

Abstract

Eukaryotic genomes are repetitively wrapped into nucleosomes that then regulate access of transcription and DNA repair complexes to DNA. The mechanisms that regulate extrinsic protein interactions within nucleosomes are unresolved. We demonstrate that modulation of the nucleosome unwrapping rate regulates protein binding within nucleosomes. Histone H3 acetyl-lysine 56 [H3(K56ac)] and DNA sequence within the nucleosome entry-exit region additively influence nucleosomal DNA accessibility by increasing the unwrapping rate without impacting rewrapping. These combined epigenetic and genetic factors influence transcription factor (TF) occupancy within the nucleosome by at least one order of magnitude and enhance nucleosome disassembly by the DNA mismatch repair complex, hMSH2–hMSH6. Our results combined with the observation that ∼30% of Saccharomyces cerevisiae TF-binding sites reside in the nucleosome entry–exit region suggest that modulation of nucleosome unwrapping is a mechanism for regulating transcription and DNA repair.

Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency

“…Nevertheless, the interaction between Oct4 and H3K56ac is unique. Previous studies have demonstrated that H3K56ac displaces nucleosomal DNA in vitro to allow DNA "breathing" (27) and access of a LexA DNA-binding protein to nucleosomal DNA (41,42). Surprisingly, our data argue not for an interaction between Oct4 and nucleosomal DNA, but for a direct interaction between Oct4 and nucleosomal H3K56ac.…”

Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

“…Whichever the route, comparison with Ets-1 indicates that excess hydration confers a significantly long-lived PU.1⅐DNA complex, a feature that may be critical to a role for PU.1 (9 -13), but not Ets-1 (14), as a pioneer transcription factor. In the dynamic nucleosomal environment, DNA accessibility in the exit-entry region of nucleosomes where cognate transcription factor binding sites are concentrated is determined by the DNA unwrapping rate (60,61). Although the relatively slow on rate for PU.1 to high affinity DNA would hinder its association to transiently accessible promoter or enhancer sites in heterochromatin, once formed, the PU.1⅐DNA complex could persist long enough to recruit other transcription factors or remodeling proteins to initiate transcription.…”

Histone Core Phosphorylation Regulates DNA Accessibility

“…The nucleosomes used in the FRET measurements were prepared as described in Ref. 27 and then purified on a 5-30% sucrose gradient. The quality of all nucleosome samples was analyzed by EMSA on 5% polyacrylamide gels (Fig.…”

“…This modification is located within promoters (19,20) and at sites of DNA repair (21); it is involved in nucleosome assembly during replication (22) and enhances transcription (23)(24)(25). H3K56ac significantly enhances the probability of DNA to partially unwrap (26) by increasing the unwrapping rate (27), which enhances DNA accessibility to proteins within the nucleosome (28,29).…”