Structural Mechanisms of Nucleosome Recognition by Linker Histones

Zhou, Bing-Rui; Jiang, Jiansheng; Feng, Hanqiao; Ghirlando, Rodolfo; Xiao, Tsan Sam; Bai, Yawen

doi:10.1016/j.molcel.2015.06.025

Cited by 206 publications

(312 citation statements)

References 58 publications

(102 reference statements)

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“…The dinucleosome represents the asymmetric unit in the structure of a tetranucleosome with one linker DNA trimmed for clarity (PDB accession number 1ZBB) (2). The H1 globular domain and its localization relative to the dyad are based on the structure of the chicken H5 globular domain in complex with a nucleosome (PDB accession number 4QLC) (33). The representation of the four-way junction is based on data reported under PDB accession number 3CRX.…”

Section: Linker Histonesmentioning

confidence: 99%

“…DNA linkers, whereas the Drosophila melanogaster linker histone H1 binds off-dyad (32,33). Experiments involving site-directed mutagenesis followed by determination of binding to nucleosomes in living cells have likewise led to the conclusion that the globular domains of different mouse H1 isoforms use different interaction surfaces for contacts to chromatin (34,35).…”

Section: Linker Histonesmentioning

confidence: 99%

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Yeast HMO1: Linker Histone Reinvented

Panday

Grove

2017

Microbiol Mol Biol Rev

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SUMMARY Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or “fragile” nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.

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Section: Linker Histonesmentioning

confidence: 99%

Section: Linker Histonesmentioning

confidence: 99%

Yeast HMO1: Linker Histone Reinvented

Panday

Grove

2017

Microbiol Mol Biol Rev

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“…At each point an atomic model of the chromatosome (PDB ID: 4QLC) 22 is aligned with the nucleosome superhelical axis tangent to the curve and its dyad axis pointing towards the opposing nucleosomes it connects. A small adjustment to entry/exit points of the chromatosome (Fig.…”

Section: Model Buildingmentioning

confidence: 99%

A metastable structure for the compact 30‐nm chromatin fibre

McGeehan

Travers

2016

FEBS Letters

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The structure of compact 30‐nm chromatin fibres is still debated. We present here a novel unified model that reconciles all experimental observations into a single framework. We propose that compact fibres are formed by the interdigitation of the two nucleosome stacks in a 2‐start crossed‐linker structure to form a single stack. This process requires that the dyad orientation of successive nucleosomes relative to the helical axis alternates. The model predicts that, as observed experimentally, the fibre‐packing density should increase in a stepwise manner with increasing linker length. This model structure can also incorporate linker DNA of varying lengths.

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“…The different structure and topology of chromatin and, therefore, its distinct functioning is determined by histone H1-DNA binding. Whereas the on-dyad axis location creates more compacted (transcriptionally inert) chromatin conformation, the off-dyad axis position forms more loosened (transcriptionally capable) chromatin structure (Zhou et al, 2015). Moreover, the mode of histone H1 binding to the DNA is determined by its C-terminal (Th'ng et al, 2005) and globular (Piscopo et al, 2010) domain and may be different in distinct cell types.…”

Section: Introductionmentioning

confidence: 99%

Evidence on the stability of histone H1.a polymorphic variants during selection in quail

Kowalski

Knaga

2017

Arch. Anim. Breed.

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Abstract. The goal of this work was to check whether selection for quantitative traits may cause a change in the histone H1 allelic complement and whether it can therefore be considered a modulator of histone H1-dependent chromatin functioning. For this purpose, a fluctuation of histone H1.a polymorphic variants was analyzed among a non-selected (control) quail line and the line selected for a high cholesterol content in the egg yolk. The histone H1.a was found to be polymorphic due to its differential migration rate in the AU-PAGE (acetic acidurea polyacrylamide gel electrophoresis). Based on this, two H1.a isoforms (H1.a1 and H1.a2) that form three phenotypes (a1, a2 and a1a2) were distinguished in the quail lines tested. A comparably expressed (p > 0.05) and low relative variable (coefficient of variation, CV < 0.25) histone H1.a phenotypes were in agreement with Hardy-Weinberg equilibrium (HWE) in both the non-selected (χ 2 = 1.29, p = 0.25) and selected (χ 2 = 1.9, p = 0.16) quail line. The similarity among quail lines was assessed based on the equal distribution of histone H1.a phenotypes (χ 2 = 1.63, p = 0.44) and alleles (χ 2 = 0.018, p = 0.89) frequency in both quail lines tested. This indicates that selection does not affect the histone H1.a polymorphic variants. The stability of histone H1.a during selection might suggest that likely chromatin processes coupled to the selected trait are not linked to the activity of histone H1.a.

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Structural Mechanisms of Nucleosome Recognition by Linker Histones

Cited by 206 publications

References 58 publications

Yeast HMO1: Linker Histone Reinvented

Yeast HMO1: Linker Histone Reinvented

A metastable structure for the compact 30‐nm chromatin fibre

Evidence on the stability of histone H1.a polymorphic variants during selection in quail

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