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Histone H3 Variants and Their Potential Role in Indexing Mammalian Genomes: the ‘‘H3 Barcode Hypothesis’’

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Histone H3 Variants and Their Potential Role in Indexing Mammalian Genomes: the ‘‘H3 Barcode Hypothesis’’ Histone H3 variants and their potential role in indexing mammalian genomes: The ‘‘H3 barcode hypothesis’’ Sandra B. Hake and C. David Allis* Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Avenue, New York, NY 10021 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected on May 3, 2005. Contributed by C. David Allis, January 31, 2006 In the history of science, provocative but, at times, controversial translated into meaningful biological responses (1, 2). The ideas have been put forward to explain basic problems that ‘‘histone code’’ hypothesis states that a specific histone modifi- confront and intrigue the scientific community. These hypotheses, cation, or combinations thereof, can affect distinct downstream although often not correct in every detail, lead to increased cellular events by altering the structure of chromatin (cis mech- discussion that ultimately guides experimental tests of the princi- anisms) or by generating a binding platform for effector proteins pal concepts and produce valuable insights into long-standing (trans mechanisms). Such effectors specifically recognize par- questions. Here, we present a hypothesis, the ‘‘H3 barcode hy- ticular PTM(s) and initiate events that ultimately lead to down- pothesis.’’ Hopefully, our ideas will evoke critical discussion and stream events, such as gene activation or silencing. Tests of this new experimental approaches that bear on general topics, such as hypothesis, as well as extensions of it (3), are gaining experi- nuclear architecture, epigenetic memory, and cell-fate choice. Our mental support (e.g., refs. 4 and 5), although alternative views hypothesis rests on the central concept that mammalian histone H3 have been expressed (6, 7). Despite these uncertainties, emerg- variants (H3.1, H3.2, and H3.3), although remarkably similar in ing evidence underscores elaborate mechanisms for introducing amino acid sequence, exhibit distinct posttranslational ‘‘signa- variation, covalent and noncovalent, into the chromatin polymer tures’’ that create different chromosomal domains or territories, (reviewed in ref. 8). The challenge remains as to how this which, in turn, influence epigenetic states during cellular differ- variation is converted into meaningful biological readout. entiation and development. Although we restrict our comments to H3 variants in mammals, we expect that the more general concepts Histone H3 Variants and Their Evolution presented here will apply to other histone variant families in With the exception of H4, all core histone proteins have variant organisms that employ them. counterparts, which often differ in surprisingly few amino acids (reviewed in ref. 9). Histone genes encoding these variants can histone H3 variants H3.1, H3.2, H3.3 ͉ ‘‘barcode hypothesis’’ ͉ epigenetic be classified into three main subtypes on the basis of their memory ͉ cell differentiation expression pattern and genomic organization (10, 11): replica- tion-dependent (RD), replication- and cell cycle phase- Chromatin and Its Role in Cellular Processes independent (RI), and tissue-specific (TS) histones. RI expres- very eukaryotic cell contains genetic information in the form sion of histone genes reinforces the general view that histone Eof DNA that is compacted to varying degrees in a confined proteins evolved to participate actively in DNA-templated pro- nuclear space. However, DNA is packaged in such a way that cesses rather than to serve simply a passive DNA-packaging role enables its readout, replication, and repair in response to cellular (see below). Nowhere is the concept of histone variants better needs and external stimuli. This condensation is achieved by an illustrated than with the family of H3 histones. intimate interaction between DNA and histone proteins to form Most eukaryotes express a centromere-specific H3 variant chromatin. The fundamental unit of chromatin is the nucleo- (Saccharomyces cerevisiae, Cse4; Drosophila, CID; and Homo some particle, consisting of core histone proteins (H2A, H2B, sapiens, CENP-A) that is evolutionarily well conserved in its H3, and H4) around which the DNA is wrapped. Chromatin is globular core region but not in its N-terminal tail (reviewed in often broadly divided into two cytologically distinct fractions: ref. 12) and is essential for cell survival because of its funda- euchromatin, which is generally permissive for transcription, and mental role in centromeric function during mitosis (13). Inter- heterochromatin, which is largely repressive. Two basic varieties estingly, during evolution, additional genes encoding H3 variants of heterochromatin exist, constitutive and facultative; DNA have emerged (Fig. 1A). For example, outside of the centromeric within constitutive heterochromatin is obligately silenced; fac- H3 variant, the unicellular yeast S. cerevisiae possesses only H3.3, ultative heterochromatin is silenced only in certain contexts. a H3 variant that is expressed and incorporated into chromatin Relevant to our proposed ‘‘H3 barcode hypothesis’’ is the in a RI fashion and associated in higher eukaryotes with extent to which the chromatin fiber is constant or variable. transcriptional activation (see below). Although budding yeast Constancy is provided by the nearly universal nucleosomal contains well defined ‘‘silent’’ chromatin, several hallmark fea- packaging theme of histones and DNA in all eukaryotes. Vari- tures of constitutive heterochromatin in higher eukaryotes (e.g., ation is provided by subtle changes in this packaging theme that H3 K9, and K27 methylation) have yet to be observed in S. provide ‘‘instructions’’ as to how the DNA template is to be cerevisiae (14). This observation correlates well with the presence ‘‘read’’ when needed. Histone proteins are, for example, well known to be extensively modified by a vast array of covalent modifications on ‘‘external’’ (N- and C-terminal tails) as well as Conflict of interest statement: No conflicts declared. ‘‘internal’’ (histone-fold) domains, often leading to complex Abbreviations: LBR, lamin B receptor; PTM, posttranslational modification; RD, replication- modification patterns that correlate closely with various states of dependent; RI, replication-independent. gene expression or other DNA-templated processes. This stag- See accompanying Profile on page 6425. gering number of posttranslational modifications (PTMs) has *To whom correspondence should be addressed. E-mail: [email protected]. prompted theories as to how these chemical marks might be © 2006 by The National Academy of Sciences of the USA 6428–6435 ͉ PNAS ͉ April 25, 2006 ͉ vol. 103 ͉ no. 17 www.pnas.org͞cgi͞doi͞10.1073͞pnas.0600803103 Downloaded by guest on September 23, 2021 modest changes in primary sequence among H3 variants unim- portant, a likely consequence of evolutionary ‘‘drift?’’ Alterna- tively, the small number of amino acid changes in these H3 INAUGURAL ARTICLE variants lead to unique protein structures and, in turn, to unique nucleosomal architecture and chromosomal domains that might govern H3 variant-specific biological functions (as is the case for centromere-associated H3s) (16). Future studies aimed at de- termining the x-ray structures of nucleosomes containing dif- ferent histone variants may provide structural insights into their effects on nucleosome stability and organization. The literature on H3 variants does not contain a universal nomenclature for these variants, and, therefore, we propose to adopt the following convention: histone H3 protein containing S31, A87, I89, and G90 will be called H3.3; H3 with A31, S87, V89, M90, and S96 will be called H3.2; and H3.1 has the sequence of H3.2, with the exception of position 96, where it contains a cysteine. Amino acids 87–90 in H3.3 have been shown to be important for RI incorporation into chromatin (17), and these data suggest that this region might act as a ‘‘chaperone recognition domain’’ where HIRA binds to H3.3 and CAF-1 to H3.1 (see below and ref. 18). It is as yet unknown whether H3.2 binds to a different chaperone and whether amino acid position 96 plays any role in this potential chaperone recognition domain (Fig. 1B). Elegant experiments have shown that H3.3 is associated with transcriptionally active gene loci and is enriched in covalent modifications associated with gene activation in flies, plants, and humans (17, 19–21). In contrast, in Drosophila and Arabidopsis, H3.2 has been shown to be enriched in marks that are associated with gene silencing (19, 20). These observations suggest that, during evolution, organisms draw on different profiles of phys- iologically relevant PTMs but also selective employment (re- Fig. 1. H3 variants in different organisms. (A) Schematic of evolutionary cruitment and replacement) of different histone H3 variants, a appearance of histone H3 variants. All organisms express a centromere- concept well articulated by Henikoff and colleagues (22). Be- specific H3 variant (CENP-A, filled blue circle). In addition to the centromeric cause H3.1 and H3.2 differ by only a single amino acid, most CELL BIOLOGY H3 variant, the following H3 variants are expressed in these organisms: S. studies tend to group these variants as one. However, recent cerevisiae contains only H3.3 (blue gradient circle); S. pombe expresses a results provide evidence that human H3.1, H3.2, and H3.3 differ hybrid H3 protein that contains amino acids characteristic for H3.3 and H3.2; in both their expression and PTM patterns
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