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There is currently no published report on the isolation and definitive identification of histone H1 in Saccharomyces cerevisiae. We showed that purified recombinant Hho1p (rHho1p) has electrophoretic and chromatographic properties similar to linker histones. The protein forms a stable ternary complex with a reconstituted core di-nucleosome in vitro at molar rHho1p:core ratios up to 1. Reconstitution of rHho1p with H1-stripped chromatin confers a kinetic pause at ϳ168 base pairs in the micrococcal nuclease digestion pattern of the chromatin. These results strongly suggest that Hho1p is a bona fide linker histone. We deleted the HHO1 gene and showed that the strain is viable and has no growth or mating defects. Hho1p is not required for telomeric silencing, basal transcriptional repression, or efficient sporulation. Unlike core histone mutations, a hho1⌬ strain does not exhibit a Sin or Spt phenotype. The absence of Hho1p does not lead to a change in the nucleosome repeat length of bulk chromatin nor to differences in the in vivo micrococcal nuclease cleavage sites in individual genes as detected by primer extension mapping.

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The importance of core histones in the regulation of DNA function by chromatin is clear. However, little is known about the role of the linker histone. We investigated the role of H1 in Saccharomyces cerevisiae during extensive transcriptional reprogramming in stationary phase. Although the levels of linker histone Hho1p remained constant during growth to semiquiescence, there was a genome-wide increase in binding to chromatin. Hho1p was essential for compaction of chromatin in stationary phase, but not for general transcriptional repression. A clear, genome-wide anticorrelation was seen between the level of bound Hho1p and gene expression. Surprisingly, the rank order of gene activity was maintained even in the absence of Hho1p. Based on these findings, we suggest that linker histone Hho1p has a limited role in transcriptional regulation and that the dynamically exchanging linker histone may be evicted from chromatin by transcriptional activity.H1 ͉ nucleosome ͉ yeast T he DNA in eukaryotes is packaged into chromatin, which is formed by arrays of a nucleoprotein complex, the nucleosome. The nucleosome is composed of Ϸ168 bp of DNA spooled as two negative superhelical coils onto a central octamer composed of two copies of each of the H2A-H2B and H3-H4 heterodimeric pairs. The repeating association of DNA with the histone octamer in chromatin renders the structure sensitive to the properties of the core histones, which are tailored by reversible chemical modifications, and by isotype permutations in octamer composition. A fifth histone, linker histone H1, binds to the outside of the nucleosome, contacting the nucleosomal DNA at positions close to the center and the ends of the superhelical gyres (1). Although this central binding of the linker histone to the nucleosome suggests an important role in the regulation of DNA function, many lower eukaryotes remain viable in the absence of a linker histone (2, 3). The continuous dynamic exchange of this histone has cast doubt on the canonical organization of the nucleosome, where the linker histone is accepted as a static structural feature (4).The involvement of H1 in the condensation of the chromatin fiber is well established. H1 was shown to be required for the salt-dependent compaction of a nucleosome array into a regular 30-nm chromatin fiber in vitro (5). This compaction of chromatin, which appears to also involve the N-terminal tail of histone H4 (6), was proposed to be due to the steady-state level of the dynamically exchanging H1 molecule.Given the connection between H1 binding and chromatin compaction, which limits unimpeded access to the DNA molecule, H1 was expected to influence global DNA function, and, in particular, gene expression, in a simple, direct manner. Surprisingly, absence of Hho1p in yeast did not result in an increase in basal transcription, as was expected for a global transcriptional repressor (3). Microarray analysis of transcription in a yeast strain in which the HHO1 gene was deleted, revealed that Ͻ1% of genes were affected by a factor of...