Transcription-induced Chromatin Remodeling at the c-myc Gene Involves the Local Exchange of Histone H2A.Z

Abstract

The post-translational modification of histones and the incorporation of core histone variants play key roles in governing gene expression. Many eukaryotic genes regulate their expression by limiting the escape of RNA polymerase from promoter-proximal pause sites. Here we report that elongating RNA polymerase II complexes encounter distinct chromatin landscapes that are marked by methylation of lysine residues Lys 4 , Lys 79 , and Lys 36 of histone H3. However, neither histone methylation nor acetylation directly regulates the release of elongation complexes stalled at promoter-proximal pause sites of the c-myc gene. In contrast, transcriptional activation is associated with local displacement of the histone variant H2A.Z within the transcribed region and incorporation of the major histone variant H2A. This result indicates that transcribing RNA polymerase II remodels chromatin in part through coincident displacement of H2A.Z-H2B dimers and incorporation of H2A-H2B dimers. In combination, these results suggest a new model in which the incorporation of H2A.Z into nucleosomes down-regulates transcription; at the same time it may act as a cellular memory for transcriptionally poised gene domains. RNA pol II1 encounters nucleosomes and other multiprotein complexes during transcription. Conceptually, any mechanism that destabilizes the DNA-histone interaction or removes part or all of the histone octamer potentially increases the elongation efficiency of RNA polymerases. Protein complexes such as FACT, Elongator, and Swi/Snf have been proposed to alleviate barriers that are imposed by chromatin (1-3). For instance, the protein complex FACT assists RNA polymerase during elongation by altering the nucleosomal conformation and destabilizing the interaction between the H2A/H2B dimer and the (H3/H4) 2 tetramer (4). After the transcription complex has passed the nucleosome, FACT participates in the reassembly of the nucleosome. In addition to the FACT-mediated catalytic remodeling of nucleosomes, the post-translational modification of histones, and/or the incorporation of histone variants also may facilitate the passage of the transcription complex through nucleosomes (5-7). For example, the identification of the acetyltransferase activity in the Elp3 subunit of the RNA pol II-associated Elongator complex suggests that histone acetylation is an important component in the regulation of transcription elongation (8,9). Indeed, previous studies demonstrated that the yeast Elongator complex is associated with nascent transcripts (2). In addition to histone acetylation, methylation of H3 lysine residues Lys -specific histone demethylase LSD1 suggests a model in which RNA polymerase II elongation is regulated by the antagonistic action of histone methyltransferases and histone demethylases (12). Alternatively, a replication-independent histone exchange pathway in which variant forms of histones are incorporated during active transcription may provide an opportunity to continuously exchange histones with either hyper-or hypomethyl...

Random deposition of histone variants: A cellular mistake or a novel regulatory mechanism?

“…In agreement with that model, Farris et al have shown that transcriptional activation of the c-myc gene is accompanied by local displacement of H2A.Z within the transcribed region and incorporation of the canonical H2A. 32 We therefore propose that random incorporation, when coupled to targeted eviction, can lead to a specific distribution pattern, just as if the SWR complex includes a protein, Bdf1, which recruits SWR to promoters by virtue of the interaction of its bromo-domain with acetylated nucleosomes. [28][29][30] In mammalian cells, two proteins have been shown to target H2A.Z to promoters.…”

Repression of Flowering inArabidopsisRequires Activation ofFLOWERING LOCUS CExpression by the Histone Variant H2A.Z

“…Several genome-wide studies of yeast H2A.Z occupancy have shown that this variant localizes to the promoters of thousands of euchromatic genes, and its presence is required for the optimal transcriptional activation of many of these genes (Guillemette et al, 2005;Li et al, 2005;Raisner et al, 2005;Zhang et al, 2005). In contrast with the situation in yeast, cytological and genetic studies suggest that in metazoans H2A.Z may also play a role in heterochromatin formation and/or maintenance (Rangasamy et al, 2003;Swaminathan et al, 2005), although this variant has been observed at the 59 ends of several active genes in human and chicken cell lines (Bruce et al, 2005;Farris et al, 2005). However, null mutations in mouse and Drosophila H2A.Z 1 To whom correspondence should be addressed.…”

Multiple microarray platforms utilized for hepatic gene expression profiling of GH transgenic coho salmon with and without ration restriction

“…Other genes involved in cell-cycle regulation (non-histone chromosome protein 2-like) and chromatin organization (histone H2A family member Z and histone H5) are also upregulated in GH transgenic liver (Table 4). Histone H2A family member Z has various functions in transcriptional regulation and maintenance of genomic stability (Farris et al 2005). Therefore, its induction in growth-enhanced salmon liver may be a part of a mechanism by which GH transgenic cells control genomic fidelity in a hyper-proliferative state.…”