Histone Release during Transcription:  Acetylation Stabilizes the Interaction of the H2A−H2B Dimer with the H3−H4 Tetramer in Nucleosomes That Are on Highly Positively Coiled DNA

Abstract

A high level of the post-translational modification, acetylation, is found on the N-terminal regions of the core histones H2A, H2B, H3, and H4 and is primarily located in the nucleosomes of active genes. An in vitro transcription system was applied, which utilizes T7 RNA polymerase and template DNAs that are either moderately or highly positively coiled, to determine whether acetylation alters the dynamics of histone displacement from these templates during transcription. To measure displacement, an excess of a competitor (negatively coiled DNA reconstituted with unlabeled H3-H4) was included during the transcription process. Acetylated but not unacetylated (3)H-labeled H3-H4 was found to displace with high frequency from the moderately positively coiled template. This displacement of acetylated H3-H4 was not observed when the template was highly positively coiled. Acetylated (3)H-labeled H2A-H2B also preferentially displaced to the competitor, but in this instance, transcription-induced stress on the highly positively coiled template was required. The histone chaperone, NAP1, was found to facilitate the displacement of both H3-H4 and H2A-H2B. Surprisingly, when acetylated H2A-H2B and acetylated H3-H4 were reconstituted together in the same nucleosomes, the displacement of acetylated H2A-H2B was much reduced during transcription. We conclude that acetylation alters nucleosome stability by enhancing displacement of H3-H4, while decreasing the displacement of H2A-H2B. These results are discussed with regard to potential in vivo conditions in which these observations may be relevant.

Global turnover of histone post-translational modifications and variants in human cells

“…Some notable examples of a direct structural effect of histone PTMs and nucleosomal structure are the electrostatic interaction between the H4 tail with respect to H2A/H2B on the adjacent nucleosome [31], the electrostatic interaction between H3K56ac and the DNA backbone [32], and the general destabilization of the nucleosome bound to positively supercoiled DNA by the hyperacetylated histones H3 and H4 [33]. The acetyl moiety removes the positive charge from lysines due to resonance effects of the carbonyl group, whereas the methyl moiety stabilizes charge by raising the acid dissociation constant (pKa) of the remaining acidic protons.…”

Reciprocal epigenetic modification of histone H2B occurs in chromatin during apoptosis in vitro and in vivo

“…It has been reported that the N-terminal tail of H2B itself is crucial for chromatin condensation25. Moreover, the H2B acetylation at the N-terminal end is important to maintain a stable structure of H2A–H2B dimers in the nucleosome26,27. Since the N-terminal domain of H2B including the S14 site exists outside of the nucleosome structure28, it could be susceptible to modification by phosphatases or kinases if left unprotected.…”

Nap1: taking a closer look at a juggler protein of extraordinary skills

“…51.) The effect of histone acetylation on the histone acceptor ability of Nap1 has been substantiated in subsequent work (102), but the exact molecular mechanism requires further investigation. Acetylation may reduce the affinity of H2A/H2B for the H3/H4 tetramer or for the DNA ends in the nucleosome (the sites of H2A/H2B binding); alternatively, acetylation may change the affinity of H2A/H2B for Nap1.…”

“…A wealth of information about the possible involvement of Nap1 in transcription elongation comes from a series of careful in vitro transcription experiments in model systems that use polynucleosomal templates re‐constituted on linear or superhelical DNA molecules of different levels of superhelical stress (102, 111, 112).…”