Centromere targeting element within the histone fold domain of Cid

Adaptive evolution of the histone fold domain in centromeric histones

Centromeric DNA, being highly repetitive, has been refractory to molecular analysis. However, centromeric structural proteins are encoded by single-copy genes, and these can be analyzed by using standard phylogenetic tools. The centromere-specific histone, CenH3, replaces histone H3 in centromeric nucleosomes, and is required for the proper distribution of chromosomes during cell division. Whereas histone H3s are nearly identical between species, CenH3s are divergent, with an N-terminal tail that is highly variable in length and sequence. Both the N-terminal tail and histone fold domain (HFD) are subject to adaptive evolution in Drosophila. Similarly, comparisons between Arabidopsis thaliana and Arabidopsis arenosa detected adaptive evolution, but only in the N-terminal tail. We have extended our evolutionary analyses of CenH3s to other members of the Brassicaceae, which allowed the detection of positive selection in both the N-terminal tail and in the HFD. We find that adaptively evolving sites in the HFD can potentially interact with DNA, including sites in the loop 1 region of the HFD that are required for centromeric targeting in Drosophila. Other adaptively evolving sites in the HFD can be localized on the structure of the nucleosome core particle, revealing an extended surface in addition to loop 1 in which conformational changes might alter histone-DNA contacts or water bridges. The identification of adaptively evolving sites provides a structural basis for the interaction between centromeric DNA and the protein that is thought to underlie the evolution of centromeres and the accumulation of pericentric heterochromatin.

Phylogenomics of the nucleosome

Histones are best known as the architectural proteins that package the DNA of eukaryotic organisms, forming octameric nucleosome cores that the double helix wraps tightly around. Although histones have traditionally been viewed as slowly evolving scaffold proteins that lack diversification beyond their abundant tail modifications, recent studies have revealed that variant histones have evolved for diverse functions. H2A and H3 variants have diversified to assume roles in epigenetic silencing, gene expression and centromere function. Such diversification of histone variants and 'deviants' contradicts the perception of histones as monotonous members of multigene families that indiscriminately package and compact the genome. How these diverse functions have evolved from ancestral forms can be addressed by applying phylogenetic tools to increasingly abundant sequence data.

Characterization of chicken CENP-A and comparative sequence analysis of vertebrate centromere-specific histone H3-like proteins

Centromere protein A (CENP-A) is a centromere-specific histone H3 variant conserved amongst all eukaryotes. We have isolated the chicken gene for CENP-A (GgCENP-A). It encodes a 131-amino-acid polypeptide that possesses an average identity of 54% with human CENP-A, reaching 69% in the histone-fold domain. The gene spans 1.7 kb of genomic DNA and contains four exons that range in size from 78 to 186 bp. The exon/intron organisation of the chicken gene is conserved with its mammalian counterparts in the carboxy-terminal histone-fold domain (exons 2 to 4), consistent with the strong conservation of this domain at the amino acid level. Sequence analysis of the chicken CENP-A locus revealed that the gene is located within the class III genes of the major histocompatibility complex (MHC), and extended the previously defined limit of the compact chicken MHC complex. We compared the sequences of CENP-A from mammals, chicken and fishes and thereby identified conserved motifs in the otherwise variable amino-terminal tail that may be important for functional reasons. We also identified evolutionarily variable regions within the conserved histone-fold domain. We found that loop 1 between the first and second alpha-helix is the region that diverged most widely. This finding is in agreement with evolutionary studies in Drosophila species, and suggests that this domain could play a role in species-specific centromere targeting of CENP-A. In addition, protein sequence comparison of several vertebrate species revealed that the RT-PCR strategy we have developed for isolating the chicken centromeric histone H3 variant gene should be applicable to the isolation of CENP-A from a wide range of vertebrates.

Stretching it: putting the CEN(P-A) in centromere

The centromere is the locus responsible for the segregation of chromosomes during mitosis and meiosis. The number of newly characterised centromere-associated proteins continues to increase. The kinetochore complex assembles at this site and in many organisms is visible as the primary constriction. In several systems the location of the site of kinetochore assembly is known to vary and the site is not specified by a strict cis-acting primary sequence. It is proposed that tension between bioriented sister centromeres may act to imprint the site.