A global requirement for the HIR complex in the assembly of chromatin

Amin, Amit Dipak; Vishnoi, Nidhi; Prochasson, Philippe

doi:10.1016/j.bbagrm.2011.07.008

Cited by 50 publications

(58 citation statements)

References 144 publications

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“…Recent data show that HIRA is in a complex that also contains calcineurin-binding protein 1 (Cabin1) and ubinuclein 1 (UBN1) (Balaji et al, 2009;Banumathy et al, 2009;Elsaesser and Allis, 2010;Rai et al, 2011). Notably, these three components have counterparts in yeast that constitute the HIR complex (Amin et al, 2011). More recently, the report of other separate H3.3 chaperones, namely DEK (Sawatsubashi et al, 2010) and a complex comprised of the death-associated protein (DAXX) and the alpha-thalassemia/mental retardation X-linked syndrome protein (ATRX) (Drané et al, 2010;Goldberg et al, 2010;Lewis et al, 2010;Wong et al, 2010) have raised the possibility that, beside the HIRA-dependent process, additional pathways could contribute to distinct H3.3 local enrichment.…”

Section: Introductionmentioning

confidence: 97%

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

et al. 2011

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Establishment of a proper chromatin landscape is central to genome function. Here, we explain H3 variant distribution by specific targeting and dynamics of deposition involving the CAF-1 and HIRA histone chaperones. Impairing replicative H3.1 incorporation via CAF-1 enables an alternative H3.3 deposition at replication sites via HIRA. Conversely, the H3.3 incorporation throughout the cell cycle via HIRA cannot be replaced by H3.1. ChIP-seq analyses reveal correlation between HIRA-dependent H3.3 accumulation and RNA pol II at transcription sites and specific regulatory elements, further supported by their biochemical association. The HIRA complex shows unique DNA binding properties, and depletion of HIRA increases DNA sensitivity to nucleases. We propose that protective nucleosome gap filling of naked DNA by HIRA leads to a broad distribution of H3.3, and HIRA association with Pol II ensures local H3.3 enrichment at specific sites. We discuss the importance of this H3.3 deposition as a salvage pathway to maintain chromatin integrity.

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Section: Introductionmentioning

confidence: 97%

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

et al. 2011

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“…Thus, the HIR complex is not a specific repressor for the histone genes. The reader is referred to Amin et al (2012b) for an in-depth review of the HIR complex.…”

Section: Negative Regulation Of the Histone Genesmentioning

confidence: 99%

Regulation of Histone Gene Expression in Budding Yeast

Eriksson¹,

Ganguli²,

Nagarajavel³

et al. 2012

Genetics

116

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We discuss the regulation of the histone genes of the budding yeast Saccharomyces cerevisiae. These include genes encoding the major core histones (H3, H4, H2A, and H2B), histone H1 (HHO1), H2AZ (HTZ1), and centromeric H3 (CSE4). Histone production is regulated during the cell cycle because the cell must replicate both its DNA during S phase and its chromatin. Consequently, the histone genes are activated in late G1 to provide sufficient core histones to assemble the replicated genome into chromatin. The major core histone genes are subject to both positive and negative regulation. The primary control system is positive, mediated by the histone gene-specific transcription activator, Spt10, through the histone upstream activating sequences (UAS) elements, with help from the major G1/S-phase activators, SBF (Swi4 cell cycle box binding factor) and perhaps MBF (MluI cell cycle box binding factor). Spt10 binds specifically to the histone UAS elements and contains a putative histone acetyltransferase domain. The negative system involves negative regulatory elements in the histone promoters, the RSC chromatin-remodeling complex, various histone chaperones [the histone regulatory (HIR) complex, Asf1, and Rtt106], and putative sequence-specific factors. The SWI/SNF chromatin-remodeling complex links the positive and negative systems. We propose that the negative system is a damping system that modulates the amount of transcription activated by Spt10 and SBF. We hypothesize that the negative system mediates negative feedback on the histone genes by histone proteins through the level of saturation of histone chaperones with histone. Thus, the negative system could communicate the degree of nucleosome assembly during DNA replication and the need to shut down the activating system under replication-stress conditions. We also discuss post-transcriptional regulation and dosage compensation of the histone genes.

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“…Both the WD40 and B domains are highly conserved in HIRA/Hir proteins from yeast to humans (Amin et al, 2012). We further found that among the seven WD40 repeats of HIRA, the first to third repeats from the N terminus (WD1 to WD3) are critically important, whereas the fifth to seventh repeats (WD5 to WD7) are not essential for the nucleosome assembly activity.…”

Section: Discussionmentioning

confidence: 68%

“…The WD40, B, and Hir domains are highly conserved in HIRA/Hir proteins (Amin et al, 2012;Lamour et al, 1995). It has been established that the B domain is required for Asf1 binding, through which histones H3 and H4 are provided to histone chaperone complexes (Tang et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

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The WD40 Domain of HIRA Is Essential for RI-nucleosome Assembly in <i>Xenopus</i> Egg Extracts

Zhu

Iwabuchi

Ohsumi

2017

Cell Struct. Funct.

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ABSTRACT. Histone chaperones are a group of histone-binding proteins that facilitate the assembly of nucleosomes, the fundamental structural units of chromatin in eukaryotes. In nucleosome assembly, deposition of a histone H3-H4 tetramer onto DNA is the first and critical step, which is mediated by the histone chaperones HIRA and CAF-1. HIRA and CAF-1 are reportedly involved in DNA replication independent (RI) and replication coupled nucleosome assembly, respectively. However, the mechanisms by which they mediate histone deposition remain unclear. In this study, we focused on the mechanism by which HIRA induces RI-nucleosome assembly. We looked for HIRA domains that are required for nucleosome assembly and its localization to chromatin. We used cell-free extracts from Xenopus eggs that carry out RI-nucleosome assembly of plasmid DNA. We confirmed that HIRA formed stable complexes with Asf1, another histone H3-H4 chaperone, and the HIRA-Asf1 complex was solely responsible for RI-nucleosome assembly in egg extracts. We further demonstrated that the HIRA N-terminus containing the WD40 domain, which comprises seven WD40 repeats, and the B domain, to which Asf1 binds, were essential for RI-nucleosome assembly; the three WD40 repeats from the Nterminus were especially critical. Using egg extracts that reproduce nuclear formation accompanying the duplication of chromatin, we also demonstrated that the Hir domain was indispensable for the binding of HIRA to chromatin. Thus, the WD40 and B domains are the core elements for inducing RI-nucleosome assembly. Hir domain regulates the binding to chromatin. Based on these findings, similarities and differences between HIRA and CAF-1 are discussed.

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A global requirement for the HIR complex in the assembly of chromatin

Cited by 50 publications

References 144 publications

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

Dynamics of Histone H3 Deposition In Vivo Reveal a Nucleosome Gap-Filling Mechanism for H3.3 to Maintain Chromatin Integrity

Regulation of Histone Gene Expression in Budding Yeast

The WD40 Domain of HIRA Is Essential for RI-nucleosome Assembly in <i>Xenopus</i> Egg Extracts

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