Abstract
BackgroundEukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. Histone H1 associates with the linker DNA to stabilize the higher-order chromatin structure and to modulate the ability of regulatory factors to access their nucleosomal targets. In Saccharomyces cerevisiae, the protein with greatest sequence similarity to H1 is Hho1p. However, during vegetative growth, hho1∆ cells do not show any discernible cell growth defects or the changes in bulk chromatin structure that are characteristic of chromatin from multicellular eukaryotes in which H1 is depleted. In contrast, the yeast high mobility group (HMGB) protein HMO1 has been reported to compact chromatin, as evidenced by increased nuclease sensitivity in hmo1∆ cells. HMO1 has an unusual domain architecture compared to vertebrate HMGB proteins in that the HMG domains are followed by a lysine-rich extension instead of an acidic domain. We address here the hypothesis that HMO1 serves the role of H1 in terms of chromatin compaction and that this function requires the lysine-rich extension.ResultsWe show here that HMO1 fulfills this function of a linker histone. For histone H1, chromatin compaction requires its basic C-terminal domain, and we find that the same pertains to HMO1, as deletion of its C-terminal lysine-rich extension renders chromatin nuclease sensitive. On rDNA, deletion of both HMO1 and Hho1p is required for significantly increased nuclease sensitivity. Expression of human histone H1 completely reverses the nuclease sensitivity characteristic of chromatin isolated from hmo1∆ cells. While chromatin remodeling events associated with repair of DNA double-strand breaks occur faster in the more dynamic chromatin environment created by the hmo1 deletion, expression of human histone H1 results in chromatin remodeling and double-strand break repair similar to that observed in wild-type cells.ConclusionOur data suggest that S. cerevisiae HMO1 protects linker DNA from nuclease digestion, a property also characteristic of mammalian linker histone H1. Notably, association with HMO1 creates a less dynamic chromatin environment that depends on its lysine-rich domain. That HMO1 has linker histone function has implications for investigations of chromatin structure and function as well as for evolution of proteins with roles in chromatin compaction.
Highlights
Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length
The C‐terminal domain of HMO1 is required for chromatin compaction To address whether the C-terminal domain of HMO1 participates in chromatin compaction in vivo during vegetative growth, as reflected in protection of linker DNA from nuclease digestion, we performed micrococcal nuclease (MNase) digestion of chromatin isolated from wild-type cells, hmo1∆, and hmo1-AB that expresses HMO1 truncated for its C-terminal tail [44]
Chromatin from hmo1-AB cells was as hypersensitive to nuclease as hmo1∆ cells (Fig. 1c), indicating that the ability to protect linker DNA requires the C-terminal domain of HMO1
Summary
Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. We address here the hypothesis that HMO1 serves the role of H1 in terms of chromatin compaction and that this function requires the lysine-rich extension. The linker DNA that separates these nucleosome core particles may associate with histone H1, much more heterogeneous proteins that condense the polynucleosome fiber [1, 2]. H1 binds the DNA that enters and exits the nucleosome and bends it as a first step toward formation of a compact structure. This binding is mediated by the globular domain, the chromatin compaction function of H1 requires its basic C-terminal extension, which organizes the linker DNA; the C-terminal domain operates as an intrinsically. Interaction of H1 with linker DNA manifests as an increased resistance to digestion by micrococcal nuclease (MNase) [9]
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