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all species have to perform a balancing act with their genome : cram it into the cell ( in the case of eukaryotes , a small part of that cell : for example , about 2 m of human dna in a nucleus of about 5 m diameter ) yet make the appropriate regions readily available for replication and expression ( and repair if something goes wrong ) .
eukaryotes achieve this feat by wrapping their dna into chromatin , a highly ordered complex with a simple repeating unit of about 146 bp dna plus eight histone proteins , termed the nucleosome .
this beads - on - a - string array is further assembled into a variety of higher - order structures all the way up to the metaphase chromosome .
the chromatin field exploded with the discovery that the monotonous - looking nucleosomes are actually hugely variable , with post - translational modifications of numerous residues on the major histones , their substitution for histone variants , and even post - translational modifications of the variants .
furthermore , the highly of dna ( such as promoters , centromeres or damaged dna ) to the appropriate enzymatic machineries .
histone variants are non - allelic isoforms of the canonical histones that can be assembled into nucleosomes in their place , and are thought thereby to provide the basis for regulation of biological processes that require local access to dna . in contrast to the s - phase - coupled synthesis of the major histones ( timing availability to the peak demand of genome replication )
histone h2a has one of the largest variant families , and includes h2a.z , a protein that is highly conserved across eukaryotes but differs considerably from the major h2a in each species ( figure 1 ) .
h2a.z has been ascribed a large number of roles , including most recently suppressing antisense rnas   and stabilizing the association of condensin with mitotic chromosomes .
although we still have a poor understanding of how the variant mediates any specific function , it is likely that differential enrichment at specific locations and distinct post - translational modifications contribute .
is monoubiquitinated , that in budding yeast ( saccharomyces cerevisiae ) is sumoylated , and in all tested species it is subject to multiple amino - terminal acetylations ( figure 1 ) , primarily by the kat5 family of acetyltransferases .
mutation of the s. cerevisiae sumoylation sites impairs movement of dna double - strand breaks to the nuclear periphery , whereas an unacetylatable allele in fission yeast ( schizosaccharomyces pombe ) recapitulates many of the phenotypes of a complete deletion . however , it is still unknown whether the effect of any of these modifications is direct ( such as steric hindrance or charge modulation influencing the formation of higher - order structures ) or indirect ( such as generating sites for the recruitment of regulatory proteins ) . a simplified view of h2a.z structure and post - translational modifications .
bars indicate the major regions of divergence between h2a.z proteins across species ( green ) and between h2a.z and h2a ( blue ) .
the relative location of the nuclear localization signal ( nls ) and regions of s. cerevisiae ( sc ) h2a.z ( called htz1 ) that mediate contact with the nap1 chaperone and the swr - complex ( swr - c ) atpase complex are also shown .
all h2a.z post - translational modifications identified so far are on the relatively divergent amino and carboxyl termini , so it is unclear whether each specific modification is invariably used to regulate variant function across species .
addition of post - translational modifications generally depends on the swr complex , indicating that each modification occurs after the variant is assembled into chromatin .
a major region of difference between h2a and h2a.z is in the loop 1 domain , which regulates interaction between the two h2a molecules in a nucleosome .
this has led to the suggestion that nucleosome core particles can only be homotypic , containing either h2a or h2a.z . however , hybrid nucleosomes containing h2a : h2b and h2a.z : h2b dimers have been observed .
the sequence of human h2a.z-1 , including the three residues that differ in h2a.z-2 , is also indicated .
the major route for h2a.z into chromatin is via swr1 , the snf2-family atpase at the catalytic center of the swr chromatin remodeling complex .
this is certainly the case in s. cerevisiae ( swr1 ) , s. pombe ( swr1 ) , humans ( srcap ) , drosophila ( domino ) and arabidopsis ( pie1 ) [ 2,3,6 - 8 ] .
the presence of h2a.z in a nucleosome facilitates intramolecular folding to higher - order arrays , particularly 30 nm chromatin fibers , although these resist the formation of more highly condensed structures resulting from intermolecular association .
h2a.z has also been reported to have a subtle destabilizing effect on the nucleosome in which it is incorporated , although this has been disputed .
the apparent contradictions in the data can however be reconciled if the total histone composition of a nucleosome octamer is considered : variants seem to subtly alter nucleosome stability , so the order of stability is h3/h2a.z = h3/h2a > h3.3/h2a > h3.3/h2a.z .
furthermore , although it was originally predicted that h2a.z was unlikely to form hybrid nucleosomes ( figure 1 ) , both homotypic ( containing two h2a.z : h2b dimers ) and heterotypic ( containing h2a : h2b and h2a.z : h2b dimers ) forms have been observed , adding yet another level of structural ( and possibly functional ) heterogeneity .
high density maps of h2a.z across genomes as diverse as s. cerevisiae , s. pombe , arabidopsis thaliana   and caenorhabditis elegans   show the variant to be widely but non - randomly distributed . in budding yeast h2a.z occupancy peaks in the single nucleosomes directly flanking ( -1/+1 ) a nucleosome - free region over promoters , a pattern apparently induced by the nucleosome - free region itself .
fission yeast , in contrast , shows enrichment in the + 1 but not the -1 nucleosome around the nucleosome - free region .
the reason for ( or outcome of ) this difference is unknown , although in each organism enrichment depends on the swr complex and is inversely correlated with transcriptional activity .
h2a.z has been linked to both transcriptional activation and repression at various genes , although consensus seems to be building towards a role in marking and/or poising promoters for expression .
the presence of h2a.z might commit local chromatin to a state competent for activation by other factors or , in higher eukaryotes , it might protect the region from inactivating dna methylation . or it might be that the cell uses the inherent instability of h2a.z - containing nucleosomes to regulate promoter accessibility .
studies on the dynamics of replication - independent histone turnover in budding yeast suggest that h2a.z - containing nucleosomes have significantly higher turnover rates .
this ' hotness ' of the nucleosomes around transcription start sites could aid promoter function by making it easier to expose these dna elements to the transcriptional machinery . such rapid flux might also abrogate the spread of a propagating domain ( such as that of the budding yeast sir2 deacetylase complex ) , which could explain how h2a.z mediates a heterochromatin - euchromatin boundary function in this organism .
h2a.z enrichment at the regions between euchromatin and heterochromatin is a feature also found in other organisms , despite the dramatic biochemical differences between the heterochromatin of budding yeast and that of many other species . in this manner
the mammalian variant is a component of pericentric heterochromatin and flanks sites occupied by the insulator binding protein ctcf .
as if the complexity described above was n't enough , recent mass spectrometry analyses of chicken erythrocytes identified two forms of h2a.z that differ by just three amino acids : h2a.z-1 ( previously h2a.z ) and h2a.z-2 ( previously h2a.f / z or h2a.v ) ( figure 1 ) .
these proteins are encoded by two non - allelic genes , which phylogenetic analyses indicate are present in all vertebrates and have a common origin early in chordate evolution .
both isoforms are incorporated into chromatin , and both seem to be acetylated on the same three lysine residues within the amino terminus ( lys4 , lys7 and lys11 ) to a similar degree ( figure 1 ) .
why would vertebrates need two copies of a protein that differ by just three amino acids , whereas invertebrates do just fine with just one ?
mouse studies ostensibly showing that h2a.z is indispensable deleted only h2a.z-1 , indicating non - redundancy : that is , h2a.z-2 can not compensate . at this stage
the three - amino - acid difference is not expected to have any major structural implication for nucleosomes .
the h2a.z isoforms could have a differential affinity for various chaperones and/or deposition machineries , which could explain their subtly different chromatin occupancy patterns .
although this might sound unlikely , there is a comparable precedent : three of the four amino acids that differ between histones h3.1 and h3.3 regulate the usage of the respective proteins in the replication - dependent and -independent deposition pathways .
however , the most important difference between h2a.z-1 and h2a.z-2 may be their highly divergent promoter sequences .
this opens up the possibility of dramatically different temporal and/or spatial expression patterns for the two isoforms . indeed ,
preliminary studies suggest some differences in mrna expression levels depending on the developmental stage of a variety of tissues . plants also have multiple h2a.z isoforms .
three have been reported in a. thaliana - hta8 , hta9 and hta11 - which share about 90% identity but have distinct expression patterns , with hta9 alone being cell - cycle - independent .
pie1 ( the plant homolog of swr1 ) interacts with all three variants , but not with h2a .
it remains to be seen whether these variants of the variant have any tissue or developmental function .
however , the parallel with vertebrates is striking and may suggest that more complex organisms need more finely tuned chromatin than one h2a.z can provide .
how much functional specialization can one component histone confer on a single nucleosome ? 
 the histone variant h2a.z seems to be an extreme example . 
 genome - wide distribution maps show non - random ( and evolutionarily conserved ) patterns , with localized enrichment or depletion giving a tantalizing suggestion of function . 
 multiple post - translational modifications on the protein indicate further regulation . 
 an additional layer of complexity has now been uncovered : the vertebrate form is actually encoded by two non - allelic genes that differ by expression pattern and three amino acids.see research articles http://www.biomedcentral.com/1741-7007/7/86 and http://www.biomedcentral.com/1471-2148/9/31 .