Histones and Histone Modifications

Magazine R546 Primer compacted metaphase domains, although more and more chromosome structures. This examples of modifications within organization of DNA into the central domains of the chromatin fibers hinders its histones have been identified Histones and accessibility to proteins that must (Figure 1). Given the number of histone ‘read’ and/or copy the nucleotide new modification sites that are base sequence, and consequently identified each year, it seems modifications such structures must be dynamic likely that nearly every histone and capable of regulated residue that is accessible to unfolding–folding transitions. solvent may be a target for post- Craig L. Peterson and Each of the core histones has a translational modification. Marc-André Laniel related globular domain that Why should histones be the mediates histone–histone target for so much enzymatic Imagine trying to stuff about interactions within the octamer, activity? Given that chromatin is 10,000 miles of spaghetti inside a and that organizes the two wraps the physiological template for all basketball. Then, if that was not of nucleosomal DNA. Each DNA-mediated processes, histone difficult enough, attempt to find a histone also harbors an amino- modifications are likely to control unique one inch segment of pasta terminal 20–35 residue segment the structure and/or function of from the middle of this mess, or that is rich in basic amino acids the chromatin fiber, with different try to duplicate, untangle and and extends from the surface of modifications yielding distinct separate individual strings to the nucleosome; histone H2A is functional consequences. Indeed, opposite ends. This simple unique in having an additional ~37 recent studies have shown that analogy illustrates some of the amino acid carboxy-terminal site-specific combinations of daunting tasks associated with domain that protrudes from the histone modifications correlate the transcription, repair and nucleosome. These histone ‘tails’ well with particular biological replication of the nearly 2 meters do not contribute significantly to functions (see Table 1). For of DNA that is packaged into the the structure of individual instance, the combination of H4 confines of a tiny eukaryotic nucleosomes nor to their stability, K8 acetylation, H3 K14 nucleus. The solution to each of but they do play an essential role acetylation, and H3 S10 these problems lies in the in controlling the folding of phosphorylation is often assembly of the eukaryotic nucleosomal arrays into higher- associated with transcription. genome into chromatin, a order structures. Indeed, in vitro Conversely, tri-methylation of H3 structural polymer that not only removal of the histone tails results K9 and the lack of H3 and H4 solves the basic packaging in nucleosomal arrays that cannot acetylation correlates with problem, but also provides a condense past the beads-on-a- transcriptional repression in dynamic platform that controls all string 10 nm fiber. Although the higher eukaryotes. Particular DNA-mediated processes within highly basic histone tails are patterns of histone modifications the nucleus. generally viewed as DNA-binding also correlate with global The basic unit of chromatin is modules, their essential roles in chromatin dynamics, as the nucleosome core particle, tail-mediated chromatin folding diacetylation of histone H4 at K4 which contains 147 bp of DNA also involve inter-nucleosomal and K12 is associated with wrapped nearly twice around an histone–histone interactions. histone deposition at S phase, octamer of the core histones. The and phosphorylation of histone histone octamer is composed of a Post-translational modifications H2A (at S1 and T119) and H3 (at central heterotetramer of histones of histones: encoding or T3, S10 and S28) appear to be H3 and H4, flanked by two patterning? hallmarks of condensed mitotic heterodimers of histones H2A and Histones are subject to an chromatin. H2B. Each nucleosome is enormous number of post- These and other observations separated by 10–60 bp of ‘linker’ translational modifications, have led to the idea of a histone DNA, and the resulting including acetylation and modification ‘code’ which might nucleosomal array constitutes a methylation of lysines (K) and be read by various cellular chromatin fiber of ~10 nm in arginines (R), phosphorylation of machineries. The term ‘code’ may diameter. This simple ‘beads-on- serines (S) and threonines (T), be a misnomer, however, as it a-string’ arrangement is folded ubiquitylation and sumoylation of implies that a particular into more condensed, ~30 nm lysines, as well as ribosylation combination of histone marks will thick fibers that are stabilized by (Figure 1; Table 1). Adding to the always dictate the same biological binding of a linker histone to each complexity is the fact that each function. By analogy, the genetic nucleosome core (note that linker lysine residue can accept one, two code is always the same no histones are not related in or even three methyl groups, and matter which gene is analyzed, in sequence to the core histones). an arginine can be either mono- or any cell type or tissue: TAG Such 30 nm fibers are then further di-methylated. The majority of always means STOP. In the case condensed in vivo to form these post-translational marks of histone modifications, however, 100–400 nm thick interphase occur on the amino-terminal and there are clear exceptions — a fibers or the more highly carboxy-terminal histone tail particular mark or set of marks Magazine R547 can have different or even opposite biological P Ac Ub consequences. For instance, the H2A Ac- S G R G K Q G G K A R A ... A V L L P K K T E S H H K A K G K -COOH generally inhibitory H3 K9 1 5 119 methylation can in some cases be associated with actively Ac AcP Ac Ac Ub transcribed genes, and histone H2B NH2- P E P V K S A P V P K K G S K K A I N K ... V K Y T S S K -COOH acetylation can be inhibitory 5 12 14 15 20 120 (123 in yeast) rather than stimulatory for Me Me Me transcription. Thus, rather than a Me P Ac Ac P P Ac MeAc Ac Me Ac P Me Me histone code there are instead clear patterns of histone marks H3 NH2- A R T K Q T A R K S T G G K A P R K Q L A S K A A R K S A ... G V K K ... E F K T D ... 2 3 4 9 10 11 14 17 18 23 262728 36 79 that can be differentially interpreted by cellular factors, depending on the gene being P MeAc Ac Ac Ac Me studied and the cellular context. H4 Ac- S G R G K G G K G L G K G G A K R H R K V L R D N I Q G I T ... 1 3 5 8 12 16 20 Current Biology Patterning chromatin: targeting the enzymes Figure 1. Post-translational modifications of the core histones. Although histone modifications The colored shapes represent known post-translational modifications of the core his- have been studied for over 30 tones. The histone tails can be methylated at lysines and arginines (green pentagons), years, the identification of the phosphorylated at serines or threonines (yellow circles), ubiquitylated (blue stars) and acetylated (red triangles) at lysines. histone modifying enzymes themselves remained elusive until the first nuclear histone SAGA interacts with the subunits that recognize DNA acetyltransferase (HAT), a transcriptional activation backbone-distorting base Tetrahymena homolog of yeast domains of a variety of yeast adducts, targeting histone H3 Gcn5, was identified in 1996. In gene-specific activator proteins, acetylation activity to sites of vivo studies in yeast had and these interactions target HAT nucleotide excision repair. previously characterized Gcn5 as activity to specific promoter A quite different strategy uses a transcriptional co-activator regions in vivo. Likewise, small noncoding RNAs to target protein, and thus its identification unliganded nuclear hormone histone H3 K9 methylation to as a HAT solidified the view that receptors interact with HDAC chromatin surrounding histone modifications directly complexes, such as NCoR and mammalian and fission yeast regulate transcription. SMRT, which direct histone centromeres. These centromeric Subsequently, a variety of other deacetylase activity to target regions are characterized by transcriptional co-activators, genes and contribute to repetitive DNA sequences that such as CBP/p300 were found to subsequent gene repression. In are transcribed at low levels. The have intrinsic HAT activity, and addition to targeting via gene- resulting double-stranded RNAs many co-repressors, such as specific regulators, the yeast provide substrates for processing Rpd3, were found to have histone Set1 and Set2 HMTs are found by the RNA interference (RNAi) deacetylation (HDAC) activity. associated with RNA polymerase machinery which produces small, Histone modification enzymes II holoenzymes, directing histone 21–23 nucleotide RNAs. Recent are now organized into large H3 K4 or K36 methylation, studies have shown that an intact HAT, HDAC, histone respectively, during RNAi pathway is essential for methyltransferase (HMT) and transcriptional elongation. targeting H3 K9 methylation to histone kinase families Targeting histone modifications centromeric chromatin, and (see Table 1). is not unique to transcriptional furthermore that these small The precise combination of control, as DNA repair and RNAs actually associate with locus-specific histone centromeric heterochromatin use several chromatin components. modifications is due to the distinct mechanisms to generate The resulting novel combined effects of targeting novel patterns of histone marks. ribonucleoprotein complex histone modifying enzymes to In the case of DNA repair, the ultimately targets the Clr4p HMT specific loci, as well as to the DNA lesion itself seems to play a to centromeric repeats, via either inherent substrate specificity of central role in targeting histone RNA–RNA (nascent centromeric the enzymes themselves.

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