Recurrent evolution of DNA-binding motifs in the
            <i>Drosophila</i>
            centromeric histone

Malik, Harmit S.; Vermaak, Danielle; Henikoff, Steven

doi:10.1073/pnas.032664299

Cited by 113 publications

(125 citation statements)

References 41 publications

(51 reference statements)

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“…The discovery that HMfA had much lower affinity than HMfB for the clone 20 sequence (27) added strong support to this idea, and the widely distributed and conserved presence of histone variants in many Eukaryotes (42) is also consistent with this concept. It is already well established that incorporation of the CENP-A family of histone H3 variants results in nucleosomes that assemble specifically at the centromere (11)(12)(13)(14)(15)(16)(17). Although unique functions have not yet been assigned to these nucleosomes, this positioning is entirely consistent with the demonstration here that very similar histone fold dimers can assemble into tetramers with structures so different that they have different DNA affinities.…”

Section: Discussionsupporting

confidence: 75%

“…Nucleosomes containing the histone H3 variant alternatively designated CENP-A, CSE4p, CID, HCP-3, or SpCENP-A (11) assemble only at centromeric DNA. Mutagenesis and domain-swap experiments have revealed that this localization is similarly dependent on a difference at the histone dimer:dimer interface in (CENPϪAϩH4) 2 and (CSE4pϩH4) 2 versus (H3ϩH4) 2 tetramers (12)(13)(14)(15)(16)(17). Based on their crystal structures, nucleosomes assembled with histones from different species or histone variants do exhibit higher order structural differences, again most notably at the sites of histone dimer:dimer interactions (18)(19)(20)(21).…”

mentioning

confidence: 99%

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Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Frederic¹,

Sandman²,

Lurz³

et al. 2002

Journal of Biological Chemistry

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DNA binding and the topology of DNA have been determined in complexes formed by >20 archaeal histone variants and archaeal histone dimer fusions with residue replacements at sites responsible for histone fold dimer:dimer interactions. Almost all of these variants have decreased affinity for DNA. They have also lost the flexibility of the wild type archaeal histones to wrap DNA into a negative or positive supercoil depending on the salt environment; they wrap DNA into positive supercoils under all salt conditions. The histone folds of the archaeal histones, HMfA and HMfB, from Methanothermus fervidus are almost identical, but (HMfA) 2 and (HMfB) 2 homodimers assemble into tetramers with sequence-dependent differences in DNA affinity. By construction and mutagenesis of HMfA؉HMfB and HMfB؉HMfA histone dimer fusions, the structure formed at the histone dimer:dimer interface within an archaeal histone tetramer has been shown to determine this difference in DNA affinity. Therefore, by regulating the assembly of different archaeal histone dimers into tetramers that have different sequence affinities, the assembly of archaeal histone-DNA complexes could be localized and used to regulate gene expression.The histone fold, three ␣-helices (␣1, ␣2, and ␣3) 1 separated by two ␤-strand loops (L1 and L2), was first identified in the four nucleosome core histones and shown to direct their assembly into (H2AϩH2B) and (H3ϩH4) heterodimers (1). Histone folds have since been found to direct the pairwise assembly of subunits in many transcription regulators, including TFIID, CBF, CHRAC, PCAF, SAGA, STAGA, and TFTC, and considerable effort has been focused on establishing the determinants of specific histone fold partnerships (2-8). In contrast, relatively few studies have investigated how such histone fold dimers are further assembled and whether alternative higher order structures might be formed with different functions or properties. It has been shown that the interface between the two (H3ϩH4) histone dimers in an (H3ϩH4) 2 tetramer is flexible and that alternative tetramer structures can result that wrap DNA in either a negative or positive DNA supercoil (9, 10). Nucleosomes containing the histone H3 variant alternatively designated CENP-A, CSE4p, CID, HCP-3, or SpCENP-A (11) assemble only at centromeric DNA. Mutagenesis and domain-swap experiments have revealed that this localization is similarly dependent on a difference at the histone dimer:dimer interface in (CENPϪAϩH4) 2 and (CSE4pϩH4) 2 versus (H3ϩH4) 2 tetramers (12-17). Based on their crystal structures, nucleosomes assembled with histones from different species or histone variants do exhibit higher order structural differences, again most notably at the sites of histone dimer:dimer interactions (18-21).Archaeal histones are only histone folds with structures almost identical to the histone folds in eukaryotic histones and transcription factors (22). They are dimers in solution but must assemble into tetramers to bind DNA (23,24). By mutagenesis, the residues have been i...

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Section: Discussionsupporting

confidence: 75%

mentioning

confidence: 99%

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Frederic¹,

Sandman²,

Lurz³

et al. 2002

Journal of Biological Chemistry

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“…Nonetheless, many of the functional components of meiosis and recombination evolve rapidly (e.g., Malik et al 2002;Anderson et al 2009;Myers et al 2010). One explanation for this rapid evolution is that meiosis and gametogenesis offer a number of opportunities for genomic conflict within an individual, generating a pattern of antagonistic coevolution between selfish gametic drivers and suppressors of meiotic drive (see Burt and Trivers 2006, for a broad overview).…”

Section: Discussionmentioning

confidence: 99%

Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

2012

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Theories to explain the prevalence of sex and recombination have long been a central theme of evolutionary biology. Yet despite decades of attention dedicated to the evolution of sex and recombination, the widespread pattern of sex differences in the recombination rate is not well understood and has received relatively little theoretical attention. Here, we argue that female meiotic drivers-alleles that increase in frequency by exploiting the asymmetric cell division of oogenesis-present a potent selective pressure favoring the modification of the female recombination rate. Because recombination plays a central role in shaping patterns of variation within and among dyads, modifiers of the female recombination rate can function as potent suppressors or enhancers of female meiotic drive. We show that when female recombination modifiers are unlinked to female drivers, recombination modifiers that suppress harmful female drive can spread. By contrast, a recombination modifier tightly linked to a driver can increase in frequency by enhancing female drive. Our results predict that rapidly evolving female recombination rates, particularly around centromeres, should be a common outcome of meiotic drive. We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex differences in recombination.

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“…It has been proposed that this coevolution will ultimately lead to incompatibilities in the form of inviability or sterility in hybrids from populations with divergent centromere machinery (Henikoff et al, 2001a). Corroboration for this 'centromere-drive' model appears to exist among Drosophila, where the main centromere-binding protein, Cid (centromere identifier), has been demonstrated to have undergone strong and recurrent adaptive evolution, presumably in response to changes in centromeric satellite sequences (Malik and Henikoff, 2001;Malik et al, 2002). However, the centromere-drive mechanism, which has the potential to act as a universal cause of divergence in almost any incipient eukaryotic species, has yet to be demonstrated to have any direct influence on naturally occurring patterns of reproductive isolation.…”

Section: Introductionmentioning

confidence: 99%

“…In Drosophila the critical centromere-specific histone gene cid has been sequenced from a number of species and is thought to have been evolving adaptively in numerous lineages for at least 25 million years (Malik et al, 2002). A dramatic recent round of selection has driven the adaptive divergence of this gene in the sister taxa Drosophila simulans and D. melanogaster (Malik and Henikoff, 2001).…”

Section: Introductionmentioning

confidence: 99%

Drosophila melanogaster and D. simulans rescue strains produce fit offspring, despite divergent centromere-specific histone alleles

et al. 2003

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The interaction between rapidly evolving centromere sequences and conserved kinetochore machinery appears to be mediated by centromere-binding proteins. A recent theory proposes that the independent evolution of centromerebinding proteins in isolated populations may be a universal cause of speciation among eukaryotes. In Drosophila the centromere-specific histone, Cid (centromere identifier), shows extensive sequence divergence between D. melanogaster and the D. simulans clade, indicating that centromere machinery incompatibilities may indeed be involved in reproductive isolation and speciation. However, it is presently unclear whether the adaptive evolution of Cid was a cause of the divergence between these species, or merely a product of postspeciation adaptation in the separate lineages. Furthermore, the extent to which divergent centromere identifier proteins provide a barrier to reproduction remains unknown. Interestingly, a small number of rescue lines from both D. melanogaster and D. simulans can restore hybrid fitness. Through comparisons of cid sequence between nonrescue and rescue strains, we show that cid is not involved in restoring hybrid viability or female fertility. Further, we demonstrate that divergent cid alleles are not sufficient to cause inviability or female sterility in hybrid crosses. Our data do not dispute the rapid divergence of cid or the coevolution of centromeric components in Drosophila; however, they do suggest that cid underwent adaptive evolution after D. melanogaster and D. simulans diverged and, consequently, is not a speciation gene.

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Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone

Cited by 113 publications

References 41 publications

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Archaeal Histone Tetramerization Determines DNA Affinity and the Direction of DNA Supercoiling

Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

Drosophila melanogaster and D. simulans rescue strains produce fit offspring, despite divergent centromere-specific histone alleles

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