Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Abstract

Summary The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem (ES) cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence, and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres, and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.

Accumulation of the FACT complex, as well as histone H3.3, serves as a target marker for somatic hypermutation

“…It is likely that the loading mechanism of FACT and H3.3 differs between Drosophila and mammals and possibly between different loci. It has been proposed that H3.3 is generally deposited to transcribed regions by the H3.3-specific histone chaperone HIRA (29,35). However, we previously showed that HIRA knockdown does not affect CSR (8).…”

Comprehensive screening of alternative lengthening of telomeres phenotype and loss of ATRX expression in sarcomas

“…13 ATRX and DAXX form a dimer that acts as a histone chaperone to deposit histone variant H3.3 to GC-rich regions of the genome, including the telomeres, and plays important roles in maintaining telomere stability. [14][15][16] It is hypothesized that dysfunction of the dimer leads to telomere instability, increased telomere homologous recombination, and ultimately, alternative lengthening of telomeres. Subsequent studies have reported frequent ATRX loss (but not DAXX loss) in astrocytoma, leiomyosarcoma, dedifferentiated liposarcoma and other tumor types, and the loss of ATRX has been highly correlated with the alternative lengthening of telomeres phenotype.…”

Histone Variant H3.3: A versatile H3 variant in health and in disease

“…However, recent genome-wide studies found that H3.3 is also deposited at heterochromatin regions such as retroviral elements, telomeres and pericentromeres (Elsasser et al, 2015;Goldberg et al, 2010). For instance, studies of mouse ES cells showed that the DAXX-dependent deposition of H3.3 at telomere regions maintains telomere integrity, a situation which is essential for self-renewal of these cells.…”

“…Meanwhile, H3.3 is also distributed in other regions such as cis-regulatory elements Goldberg et al, 2010;Mito et al, 2007), and plays an important part in the regulation of gene expression . However, the chaperon that is responsible for deposition of H3.3 at these regions remains to be identified (Filipescu et al, 2013;Goldberg et al, 2010;Szenker et al, 2011). Taken together, these results suggest that H3.3 is deposited across the genome by dedicated chaperone pathways with respect to chromatin contexts ( Figure 1B).…”

“…Moreover, in recent studies in mouse ES cells using chromatin immunoprecipitation combined with high-resolution genome-wide sequencing (ChIP-seq), it was revealed that H3.3 is also enriched at a subset of inactive genes, telomeres and repetitive elements such as endogenous retroviral elements (ERVs) (Elsasser et al, 2015;Goldberg et al, 2010), where ATRX/DAXX is required for H3.3 deposition and the maintenance of a repressive chromatin state (Elsasser et al, 2015;Goldberg et al, 2010;Lewis et al, 2010;Voon et al, 2015). Meanwhile, H3.3 is also distributed in other regions such as cis-regulatory elements Goldberg et al, 2010;Mito et al, 2007), and plays an important part in the regulation of gene expression . However, the chaperon that is responsible for deposition of H3.3 at these regions remains to be identified (Filipescu et al, 2013;Goldberg et al, 2010;Szenker et al, 2011).…”