Inducible Deposition of the Histone Variant H3.3 in Interferon-stimulated Genes

Abstract

Recent studies of the histone H3.3 variant indicate that it is incorporated into nucleosomal chromatin in association with active gene expression (1-4). Although other H3 variants, H3.1 and H3.2, are synthesized predominantly in S phase and are deposited onto newly replicated DNA, H3.3 is synthesized throughout the cell cycle, independent of DNA replication. Replication-independent incorporation of H3.3 is mediated by the HIRA complex, through a mechanism distinct from that of replication-dependent deposition of H3.1 mediated by the CAF1 complex (5). In Drosophila as well as in mammalian cells, H3.3 is enriched in nucleosomes carrying post-translational modification patterns characteristic of active transcription (6, 7). On the other hand, H3K9 dimethylation, typically seen in transcriptionally repressed chromatin, is scarce in H3.3. Histone H3.3 is accumulated in the transcriptionally active ribosomal DNA array in the Drosophila nucleus (8). A genome-wide analysis of H3.3 distribution patterns showed that H3.3 is distributed predominantly over regions of active genes and is enriched in the promoter regions coinciding with methylated Lys-4 in H3 and abundant RNA polymerase II binding (9). These studies led to a proposition that H3.3 marks active chromatin and may be involved in the epigenetic maintenance of chromatin status (3, 10 -12). Evidence supporting the role of H3.3 in the inheritance of activated gene status was recently presented by nuclear transplantation experiments in Xenopus (13).It has been shown that H3.3 replacement is triggered upon transcriptional activation of the HSP 70 genes in Drosophila (14). In that study, H3.3 deposition began within minutes of heat shock stimulation. This induced deposition coinciding with chromosomal puffs, providing an immediate link between transcription and H3.3 enrichment. Further supporting transcription-coupled H3.3 deposition, Janicki et al. (15) Despite these studies, there are questions that have remained uncertain regarding H3.3 incorporation. For example, it is unclear whether transcriptional activation is a prerequisite of H3.3 deposition. Also unclear is the stability of transcriptioninduced H3.3 deposition as well as the spatial patterns of H3.3 incorporation within induced genes. In addition, the biological significance of transcription-coupled H3.3 enrichment has remained elusive.With respect to the sites of H3.3 enrichment within a gene, widely varied results are reported for vertebrate cells, ranging from promoter-biased H3.3 incorporation to broader distribution patterns that include coding regions (16,17). A study by Jin and Felsenfeld (18) on chicken erythroid cells concluded that there is no straightforward correlation between gene expression and H3.3 enrichment.In this report, we have studied interferon (IFN)-dependent transcription as a model to address signal-induced H3.3

Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres

“…Viewed in a broader context, our results raise the question of whether newly incorporated H3.3 serves a specialized role beyond simply replacing the "old" histone H3. While it has been proposed that H3.3 nucleosomes are intrinsically less stable (43) and promote transcription (44), the exact role of transcription in heterochromatin still remains unclear and poorly defined. Others and we have observed mitotic phosphorylation of H3.3 S31 at ESC telomeres as well as pericentric heterochromatin of differentiated cells (10,27).…”

The double face of the histone variant H3.3

“…These studies revealed specific enrichment of H3.3 throughout the gene body of transcribed genes as well as at the promoter regions ( Figure 3) [24,31,[36][37][38][39][40]. H3.3 enrichment at promoters has been observed not only at active but also at inactive genes, possibly accounting for a poised state of these genes [40,41]. Furthermore, H3 replacement by the H3.3 variant also occurs at genic and intergenic regulatory regions in various metazoans [40,42,43].…”

Myogenic transcriptional activation of MyoD mediated by replication-independent histone deposition

“…Indeed, transcription induction coincides with H3.3 accumulation at several individual genes (20)(21)(22). However, recent reports based on detailed analysis of transcriptional and developmental phenotypes of flies that have been genetically manipulated to deplete H3.3 have challenged its functional significance in active transcription (23,24), because H3.3 was dispensable for most transcriptional events throughout Drosophila development.…”