Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-Responsive Genes▿

Institute for Systems Biology, 1441 N 34th St., Seattle, WA 98103, USA.
Molecular and Cellular Biology (Impact Factor: 4.78). 04/2009; 29(9). DOI: 10.1128/MCB.01233-08
Source: PubMed Central


The histone variant H2A.Z (Htz1p) has been implicated in transcriptional regulation in numerous organisms, including Saccharomyces cerevisiae. Genome-wide transcriptome profiling and chromatin immunoprecipitation studies identified a role for Htz1p in the rapid and
robust activation of many oleate-responsive genes encoding peroxisomal proteins, in particular POT1, POX1, FOX2, and CTA1. The Swr1p-, Gcn5p-, and Chz1p-dependent association of Htz1p with these promoters in their repressed states appears to establish
an epigenetic marker for the rapid and strong expression of these highly inducible promoters. Isw2p also plays a role in establishing
the nucleosome state of these promoters and associates stably in the absence of Htz1p. An analysis of the nucleosome dynamics
and Htz1p association with these promoters suggests a complex mechanism in which Htz1p-containing nucleosomes at fatty acid-responsive
promoters are disassembled upon initial exposure to oleic acid leading to the loss of Htz1p from the promoter. These nucleosomes
reassemble at later stages of gene expression. While these new nucleosomes do not incorporate Htz1p, the initial presence
of Htz1p appears to mark the promoter for sustained gene expression and the recruitment of TATA-binding protein.

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    • "For each chromatin immunoprecipitation experiment, yeast strains were grown in the YPD medium to an OD600 of 1.0. ChIP was performed as described previously [35]. In brief, proteins were cross-linked to their respective DNA-binding sites with 1% (v/v) formaldehyde for 1 h at room temperature. "
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    ABSTRACT: Histone variant Htz1 substitution for H2A plays important roles in diverse DNA transactions. Histone chaperones Chz1 and Nap1 (nucleosome assembly protein 1) are important for the deposition Htz1 into nucleosomes. In literatures, it was suggested that Chz1 is a Htz1-H2B-specific chaperone, and it is relatively unstructured in solution but it becomes structured in complex with the Htz1-H2B histone dimer. Nap1 (nucleosome assembly protein 1) can bind (H3-H4)2 tetramers, H2A-H2B dimers and Htz1-H2B dimers. Nap1 can bind H2A-H2B dimer in the cytoplasm and shuttles the dimer into the nucleus. Moreover, Nap1 functions in nucleosome assembly by competitively interacting with non-nucleosomal histone-DNA. However, the exact roles of these chaperones in assembling Htz1-containing nucleosome remain largely unknown. In this paper, we revealed that Chz1 does not show a physical interaction with chromatin. In contrast, Nap1 binds exactly at the genomic DNA that contains Htz1. Nap1 and Htz1 show a preferential interaction with AG-rich DNA sequences. Deletion of chz1 results in a significantly decreased binding of Htz1 in chromatin, whereas deletion of nap1 dramatically increases the association of Htz1 with chromatin. Furthermore, genome-wide nucleosome-mapping analysis revealed that nucleosome occupancy for Htz1p-bound genes decreases upon deleting htz1 or chz1, suggesting that Htz1 is required for nucleosome structure at the specific genome loci. All together, these results define the distinct roles for histone chaperones Chz1 and Nap1 to regulate Htz1 incorporation into chromatin.
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    • "Inactivation of INO80 leads to mislocalization of histone H2A.Z to transcribed regions (41). Interestingly, this histone variant was found to be involved in TBP recruitment (48,49), which could be altered by Ino80p depletion. Alternatively, Mot1p and NC2 might have direct functions in DNA repair and replication, as is the case for the INO80 complex (41,42). "
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    ABSTRACT: Chromatin structure in transcribed regions poses a barrier for intragenic transcription. In a comprehensive study of the yeast chromatin remodelers and the Mot1p-NC2 regulators of TATA-binding protein (TBP), we detected synthetic genetic interactions indicative of suppression of intragenic transcription. Conditional depletion of Mot1p or NC2 in absence of the ISW1 remodeler, but not in the absence of other chromatin remodelers, activated the cryptic FLO8 promoter. Likewise, conditional depletion of Mot1p or NC2 in deletion backgrounds of the H3K36 methyltransferase Set2p or the Asf1p-Rtt106p histone H3-H4 chaperones, important factors involved in maintaining a repressive chromatin environment, resulted in increased intragenic FLO8 transcripts. Activity of the cryptic FLO8 promoter is associated with reduced H3 levels, increased TBP binding and tri-methylation of H3K4 and is independent of Spt-Ada-Gcn5-acetyltransferase function. These data reveal cooperation of negative regulation of TBP with specific chromatin regulators to inhibit intragenic transcription.
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    • "In plants nucleoporins have been found necessary to survive cold stress [42], and essential for the symbiosis with mycorrhizal fungi [43]. Swr1p is a member of the Swi2/SNF2 family of ATP-dependent chromatin remodelling enzymes [44], and it regulates the deposition of histone at repressed promoters and allows for the rapid activation of transcription in yeast [45]. A gene encoding a SNF2 domain-containing protein was identified as dehydration-upregulated in the resurrection plant Xerophyta humilis[32]. "
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