Histone variants and epigenetics

Abstract

Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.

Figure 1.

Histone variants. Protein domain structure for the core histones (H3, H4, H2A, and H2B), linker histone H1, and variants of histones H3 and H2A. The histone-fold domain (HFD) is where histone dimerization occurs. Regions of sequence variation in histone variants are indicated in red. WHD, winged-helix domain.

Figure 2.

Archaeal cladogram indicating the presence of histones in all ancestral clades. Losses are attributable to horizontal transfer of HU proteins from bacteria. (Modified, with permission, from Brochier-Armanet et al. 2011, © Elsevier.)

Figure 3.

Location of histones H3 (blue) and H2A (brown) in the nucleosome core particle. Differences between variants are highlighted in yellow. (Reprinted, with permission, from Henikoff and Ahmad 2005.)

Figure 4.

Distribution of old and new nucleosomes at a replication fork. Old nucleosomes (gray disks) are randomly distributed behind the replication fork and new nucleosomes (cyan disks) are deposited in the gaps. CAF-1-mediated nucleosome assembly is depicted on the leading and lagging strand in magnification. DNA polymerase (green); replication processivity clamp, PCNA (gray ring); histone H3-H4 tetramers (cyan); newly synthesized DNA (red lines).

Figure 5.

cenH3s at centromeres of eukaryotes. (A) Human neocentromeres (indicated by an arrow) lack centromeric α-satellite DNA, but have CENP-A and heterochromatin. Anti-CENP-A staining in green and Anti-CENP-B staining in red (which marks α-satellite DNA) identifies a Chromosome 4 neocentromere that lacks α-satellite (main panel). This Chromosome 4 is otherwise normal, having been transmitted for at least three meiotic generations in normal individuals. Inset shows anti-HP1 staining, which indicates that despite the lack of satellite DNA, heterochromatin forms around active neocentromeres (indicated by arrow). (Reprinted, with permission, from Amor et al. 2004a, © National Academy of Sciences.) (B) Drosophila melanogaster anti-cenH3 antibody (red) stains centromeres in metaphase chromosomes and throughout interphase. (Image courtesy of Suso Platero.) (C) C. elegans anti-cenH3 antibody (green) stains the end-to-end holocentromeres of prophase chromosomes (red). (Image courtesy of Landon Moore.)

Figure 6.

Histone variant phylogenies. Histone sequences from selected species were multiply aligned and neighbor-joining trees were produced using the EBI server (http://www.ebi.ac.uk/Tools/phylogeny). (A) Histone H3s. (B) Histone H2As. Note that there are no clear phylogenetic distinctions between RC H3 and RI H3.3, and between RC H2A and RI H2A.X. (C) H1 variants from diverse eukaryotes show a “star” phylogeny, which suggests that they are functionally interchangeable. (C, Modified from Talbert et al. 2012.)

Figure 7.

H3.3 preferentially localizes to actively transcribed regions of Drosophila polytene chromosomes. DAPI staining (red) shows the DNA banding pattern (left), and H3.3-GFP (green) localizes to interbands (middle), which are sites of RNA Pol II localization. The merge (Schwartz and Ahmad 2005) is shown on the right. In each image, the shorter arrow points to a decondensed interband that is enriched in H3.3, and the longer arrow points to a condensed band that lacks H3.3.

Figure 8.

Model for maintenance of histone modifications by the concerted action of multiple chromatin regulators via RI replacement with H3.3. We address the question of how a histone modification can be inherited when a nucleosome is lost and replaced. (A) The Suv39h H3K9 methyltransferase (an ortholog of fly Su(var)3-9) is recruited by HP-1 protein, which binds specifically to methylated H3K9. To perpetuate this mark when the nucleosome turns over, we speculate that the ATRX ATPase is recruited to the site via its ATRX-DNMT3-DNMT3L (ADD) domain, which binds with high specificity to methylated H3K9 on tails that entirely lack H3K4 methylation (because there are no H3K4 methyltransferases in this region of the genome). (B) ATRX provides the energy of ATP and works together with the H3.3-specific DAXX histone chaperone complex to incorporate the new nucleosome (Goldberg et al. 2010), or half-nucleosome in the case of partial eviction (Xu et al. 2010). The high local concentration of Suv39h results in a new nucleosome with the same H3K9 methylation as the nucleosome that was lost.

Figure 9.

Models for RI replacement or exchange. A large molecular machine (either the SWR1 complex or RNA polymerase) partially or completely unravels a nucleosome during transit. The result is either retention of heterodimeric subunits, such as the FACT-facilitated transfer of H2A-H2B from in front of RNA polymerase to behind (Formosa et al. 2002; Belotserkovskaya et al. 2003) or loss of a heterodimer. In the latter case, chromatin repair replaces the lost heterodimer with either H3.3-H4 (left) or H2A.Z-H2B (right).

Figure 10.

Pachytene stage of spermatogenesis showing the dependence of sex-body formation on H2A.X. In normal mammalian spermatocytes, a nuclear structure, the sex body (arrow, green, in right panels), is seen to encompass the unpaired XY bivalent (labeled in left panels). The synaptonemal complex, which aligns paired chromosomes, is stained red. H2A.X is normally enriched in the sex body (H2A.X^+/+). In H2A.X^−/− spermatocytes, the sex body does not form and a sex-body epitope becomes dispersed (lower right). Scale bar, 10 µm. (Images courtesy of Shantha Mahadevaiah and Paul Burgoyne; Fernandez-Capetillo et al. 2003.)

Figure 11.

H2A variants and the inactive X chromosome of human females. (A) macroH2A (red) stains discrete regions of the inactive X chromosome that alternate with a marker for heterochromatin (histone H3K9me3). (B) H2A.B (green) is excluded from the inactive X chromosome (red dot with arrowhead pointing to it). (C) Same nucleus as in B, but stained with DAPI to show chromatin. (A, Reprinted, with permission, from Chadwick and Willard 2004, © National Academy of Sciences; B,C, reprinted, with permission, from Chadwick and Willard 2001, © 2001 The Rockefeller University Press. Originally published in Journal of Cell Biology 152: 375–384. doi: 10.1083/jcb.152.2.375.)