2
histone exchange 6 . The enzymes that medi- ate these modifications are often members of large protein complexes that are recruited to DNA by site-specific binding proteins to facilitate or impede a biological process. In the case of yeast Isw2, its best-understood func- tions are sliding nucleosomes 6 — even onto energetically unfavourable DNA sequences 7 — and repressing transcription 8 . But, like similar proteins in multicellular eukaryotes, the functions of Isw2 probably extend to processes other than transcription 6 . Studying Isw2, Whitehouse et al. 1 provide the first global analysis of nucleosome positioning in a eukaryote lacking a chromatin-remodel- ling factor. The authors used genome-tiling arrays to map nucleosome positions in both normal and Isw2-deficient yeast strains. They then compared this analysis with genome- wide measurements of RNA levels in ISW2 mutants and the localization of the Isw2 protein in the normal strain. The result is a comprehensive, high-resolution view of where on the yeast genome Isw2 localizes, where it directs changes in chromatin and where it alters transcription. A fascinating picture emerges: the role of Isw2 in altering nucleosome position is global, with this remodelling factor regulating chro- matin patterns in more than 1,000 genomic regions. Isw2 physically associates with many of these regions, which implies that it has direct effects on chromatin and transcription. Although removal of Isw2 might have altered nucleosome positioning at random locations in the genome, Whitehouse et al. observe a much more interesting pattern. They find a strong bias for Isw2 action and association at the 5ʹ and 3ʹ ends of genes. Strikingly, ISW2 dele- tion caused nucleosomes that normally lie at the boundary of intergenic and coding regions to shift towards the coding regions. This shift was detected irrespectively of whether Isw2 was functioning at the 5ʹ or the 3ʹ end of a gene. Like a sliding-tile puzzle, the normal function of Isw2 is to slide nucleosomes towards inter- genic regions, thus restricting the accessibility of these regions (Fig. 1). At the 5ʹ end of genes, Isw2 slides nucleo- somes towards the promoter, potentially obscuring the transcription start site, as well as the binding sites for regulatory factors; this would repress transcription. But what is the function of Isw2 at the 3ʹ end of genes? In strains lacking Isw2, the authors observed increased antisense transcription at the 3ʹ ends of several genes (that is, transcription in the opposite direction to the gene sequence). So Isw2 seems to play a central part in guarding the transcriptional integrity of the genome by preventing inappropriate initiation of tran- scription from within intergenic regions both in the sense and antisense directions. Whitehouse and colleagues’ work also raises many questions. For example, how is the func- tion of Isw2 focused on the borders between intergenic and coding sequences? Although MATERIALS CHEMISTRY Cool conditions for mobile ions Michael A. Hayward and Matthew J. Rosseinsky A complex iron oxide has been made that has an unusual crystal structure suggesting that the oxide ions are surprisingly mobile. This finding could pave the way to other metal-oxide materials with useful properties. Transition-metal compounds provide a ‘double whammy’ of interest for researchers. Not only do they offer the fundamental scientific chal- lenge of finding ways to control and enhance their properties, but they also have applications in such diverse areas as catalysis, magnetic information storage and battery technology. Reporting in this issue (page 1062), Tsujimoto et al. 1 describe how a previously unknown kind of mixed metal oxide can be made by side-stepping the thermodynamic limitations of traditional syntheses using a recently dis- covered method. This achievement opens the door to synthesis of many other complex metal oxides that have potentially useful properties. The hallmark of transition metals is their ability to adopt a range of charged states, in which their outermost atomic orbitals (d orbi- tals) are only partly occupied by electrons. These electrons interact with ligands — neigh- bouring ions or molecules that bind to the metal — so that both the d-electron count and the number and arrangement of the ligands determine the electronic configuration of the metal. The electronic configuration in turn controls such properties as the colour or chemical reactivity of an isolated metal–ligand complex. When the transition-metal ions form part of a crystalline solid, ligands can be shared between metal atoms. This allows the d elec- trons on neighbouring metals to interact with each other, producing cooperative electronic properties 2 such as magnetic order or high- temperature superconductivity. Ligands tend to have a limited repertoire of arrangements around metals, and these are determined by the number of d electrons available. In the search for materials with unu- sual properties, finding compounds with new arrangements of ligands around metals with a given number of d electrons is crucial. This is just what Tsujimoto et al. 1 have done in their discovery of SrFeO 2 . The authors’ new compound is an example of a complex oxide — that is, an oxide that contains more than one type of metal cat- ion, in this case strontium (Sr 2+ ) and iron (Fe 2+ ). Surprisingly, each Fe 2+ ion is surrounded by four oxide ions (O 2– ) arranged in a square, so that the whole complex is planar. This ligand geometry is expected to be highly unfavourable for Fe 2+ ions in a complex oxide 3 . In the solid form of SrFeO 2 , the iron oxide squares join together to form sheets like molec- ular patchwork quilts, in which oxide ligands are shared between Fe 2+ ions (Fig. 1). The sheets, interleaved with layers of strontium ions to balance the overall charge, stack up to yield an ‘infinite layer’ structure. This ionic assem- bly is of great interest, because it is adopted by many copper oxide superconductors 4 — but it has never been observed for an iron oxide before. So why not? To answer this question, one needs to chromatin-remodelling factor will motivate similar studies on other such factors. Undoubt- edly, more surprises are in store. Karen M. Arndt is in the Department of Biological Sciences, 269 Crawford Hall, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA. e-mail: [email protected] 1. Whitehouse, I., Rando, O. J., Delrow, J. & Tsukiyama, T. Nature 450, 1031–1035 (2007). 2. Yuan, G.-C. et al. Science 309, 626–630 (2005). 3. Lee, W. et al. Nature Genet. 39, 1235–1244 (2007). 4. Segal, E. et al. Nature 442, 772–778 (2006). 5. Ioshikhes, I. P., Albert, I., Zanton, S. J. & Pugh, B. F. Nature Genet. 38, 1210–1215 (2006). 6. Saha, A., Wittmeyer, J. & Cairns, B. R. Nature Rev. Mol. Cell Biol. 7, 437–447 (2006). 7. Whitehouse, I. & Tsukiyama, T. Nature Struct. Mol. Biol. 13, 633–640 (2006). 8. Goldmark, J. P., Fazzio, T. G., Estep, P. W., Church, G. M. & Tsukiyama, T. Cell 103, 423–433 (2000). 9. Raisner, R. M. & Madhani, H. D. Curr. Opin. Genet. Dev. 16, 119–124 (2006). 10. Alén, C. et al. Mol. Cell 10, 1441–1452 (2002). certain DNA-binding repressor proteins are known to recruit Isw2 to promoters 8 , the large number of genes affected by the absence of this chromatin-remodelling factor indicates that other mechanisms exist. Does the histone protein H2A.Z, which selectively occupies the first nucleosome downstream of the transcrip- tion start site 9 , have a part in Isw2 recruitment or activity? What mechanisms localize Isw2 to the 3ʹ ends of genes? Is the previously reported connection between Isw2 and termination of transcription 10 due to the effects of this factor on nucleosome positioning or on antisense transcription? From a mechanistic standpoint, understand- ing how Isw2 generates a directional shift in nucleosomes, how its effects are limited to the first three nucleosomes of a gene, and how it blocks transcription will be exciting problems to address. It is also hoped that the insight gained by this comprehensive analysis 1 of one 960 NATURE|Vol 450|13 December 2007 NEWS & VIEWS

Materials chemistry: Cool conditions for mobile ions

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  • histone exchange6. The enzymes that medi-ate these modifications are often members of large protein complexes that are recruited to DNA by site-specific binding proteins to facilitate or impede a biological process. In the case of yeast Isw2, its best-understood func-tions are sliding nucleosomes6 even onto energetically un favourable DNA sequences7 and repressing transcription8. But, like similar proteins in multicellular eukary otes, the functions of Isw2 probably extend to processes other than transcription6.

    Studying Isw2, Whitehouse et al.1 provide the first global analysis of nucleosome positioning in a eukaryote lacking a chromatin-remodel-ling factor. The authors used genome-tiling arrays to map nucleosome positions in both normal and Isw2-deficient yeast strains. They then compared this analysis with genome-wide measurements of RNA levels in ISW2 mutants and the localization of the Isw2 protein in the normal strain. The result is a comprehensive, high-resolution view of where on the yeast genome Isw2 localizes, where it directs changes in chromatin and where it alters transcription.

    A fascinating picture emerges: the role of Isw2 in altering nucleosome position is global, with this remodelling factor regulating chro-matin patterns in more than 1,000 genomic regions. Isw2 physically associates with many of these regions, which implies that it has direct effects on chromatin and transcription. Although removal of Isw2 might have altered nucleosome positioning at random locations in the genome, Whitehouse et al. observe a much more interesting pattern. They find a strong bias for Isw2 action and association at the 5 and 3 ends of genes. Strikingly, ISW2 dele-tion caused nucleosomes that normally lie at the boundary of intergenic and coding regions to shift towards the coding regions. This shift was detected irrespectively of whether Isw2 was functioning at the 5 or the 3 end of a gene. Like a sliding-tile puzzle, the normal function of Isw2 is to slide nucleosomes towards inter-genic regions, thus restricting the accessibility of these regions (Fig. 1).

    At the 5 end of genes, Isw2 slides nucleo-somes towards the promoter, potentially obscuring the transcription start site, as well as the binding sites for regulatory factors; this would repress transcription. But what is the function of Isw2 at the 3 end of genes? In strains lacking Isw2, the authors observed increased antisense transcription at the 3 ends of several genes (that is, transcription in the opposite direction to the gene sequence). So Isw2 seems to play a central part in guarding the transcriptional integrity of the genome by preventing inappropriate initiation of tran-scription from within intergenic regions both in the sense and antisense directions.

    Whitehouse and colleagues work also raises many questions. For example, how is the func-tion of Isw2 focused on the borders between intergenic and coding sequences? Although

    MATERIALS CHEMISTRY

    Cool conditions for mobile ionsMichael A. Hayward and Matthew J. Rosseinsky

    A complex iron oxide has been made that has an unusual crystal structure suggesting that the oxide ions are surprisingly mobile. This finding could pave the way to other metal-oxide materials with useful properties.

    Transition-metal compounds provide a double whammy of interest for researchers. Not only do they offer the fundamental scientific chal-lenge of finding ways to control and enhance their properties, but they also have applications in such diverse areas as catalysis, magnetic information storage and battery technology. Reporting in this issue (page 1062), Tsuji moto et al.1 describe how a previously unknown kind of mixed metal oxide can be made by side-stepping the thermodynamic limitations of traditional syntheses using a recently dis-covered method. This achievement opens the door to synthesis of many other complex metal oxides that have potentially useful properties.

    The hallmark of transition metals is their ability to adopt a range of charged states, in which their outermost atomic orbitals (d orbi-tals) are only partly occupied by electrons. These electrons interact with ligands neigh-bouring ions or molecules that bind to the metal so that both the d-electron count and the number and arrangement of the ligands determine the electronic configuration of the metal. The electronic configuration in turn controls such properties as the colour or chemical reactivity of an isolated metalligand complex. When the transition-metal ions form part of a crystalline solid, ligands can be shared between metal atoms. This allows the d elec-trons on neighbouring metals to interact with each other, producing cooperative electronic

    properties2 such as magnetic order or high-temperature superconductivity.

    Ligands tend to have a limited repertoire of arrangements around metals, and these are determined by the number of d electrons available. In the search for materials with unu-sual properties, finding compounds with new arrangements of ligands around metals with a given number of d electrons is crucial. This is just what Tsujimoto et al.1 have done in their discovery of SrFeO2.

    The authors new compound is an example of a complex oxide that is, an oxide that contains more than one type of metal cat-ion, in this case strontium (Sr2+) and iron (Fe2+). Sur prisingly, each Fe2+ ion is surrounded by four oxide ions (O2) arranged in a square, so that the whole complex is planar. This ligand geometry is expected to be highly unfav ourable for Fe2+ ions in a complex oxide3.

    In the solid form of SrFeO2, the iron oxide squares join together to form sheets like molec-ular patchwork quilts, in which oxide ligands are shared between Fe2+ ions (Fig. 1). The sheets, interleaved with layers of strontium ions to balance the overall charge, stack up to yield an infinite layer structure. This ionic assem-bly is of great interest, because it is adopted by many copper oxide superconductors4 but it has never been observed for an iron oxide before. So why not?

    To answer this question, one needs to

    chromatin-remodelling factor will motivate similar studies on other such factors. Undoubt-edly, more surprises are in store. Karen M. Arndt is in the Department of Biological Sciences, 269 Crawford Hall, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA.e-mail: [email protected]

    1. Whitehouse, I., Rando, O. J., Delrow, J. & Tsukiyama, T. Nature 450, 10311035 (2007).

    2. Yuan, G.-C. et al. Science 309, 626630 (2005).3. Lee, W. et al. Nature Genet. 39, 12351244 (2007).4. Segal, E. et al. Nature 442, 772778 (2006).5. Ioshikhes, I. P., Albert, I., Zanton, S. J. & Pugh, B. F.

    Nature Genet. 38, 12101215 (2006).6. Saha, A., Wittmeyer, J. & Cairns, B. R. Nature Rev. Mol. Cell

    Biol. 7, 437447 (2006).7. Whitehouse, I. & Tsukiyama, T. Nature Struct. Mol. Biol. 13,

    633640 (2006).8. Goldmark, J. P., Fazzio, T. G., Estep, P. W., Church, G. M.

    & Tsukiyama, T. Cell 103, 423433 (2000).9. Raisner, R. M. & Madhani, H. D. Curr. Opin. Genet. Dev. 16,

    119124 (2006).10. Aln, C. et al. Mol. Cell 10, 14411452 (2002).

    certain DNA-binding repressor proteins are known to recruit Isw2 to promoters8, the large number of genes affected by the absence of this chromatin-remodelling factor indicates that other mechanisms exist. Does the histone protein H2A.Z, which selectively occupies the first nucleosome downstream of the transcrip-tion start site9, have a part in Isw2 recruitment or activity? What mechanisms localize Isw2 to the 3 ends of genes? Is the previously reported connection between Isw2 and termination of transcription10 due to the effects of this factor on nucleosome positioning or on antisense transcription?

    From a mechanistic standpoint, understand-ing how Isw2 generates a directional shift in nucleosomes, how its effects are limited to the first three nucleosomes of a gene, and how it blocks transcription will be exciting problems to address. It is also hoped that the insight gained by this comprehensive analysis1 of one

    960

    NATURE|Vol 450|13 December 2007NEWS & VIEWS

  • consider the differences between solid-state reactions and those that occur in solution. Reactions in solution can be performed at low temperatures, because molecular diffusion occurs easily and the reacting molecules dont require much energy to mix together. Under these conditions, if a molecule can take part in several reactions, only the one with the low-est energy barrier to activation tends to occur. The product of such a kinetically controlled reaction is the one that forms fastest, and is not necessarily the one that is most stable. It is therefore possible to control reactions in solu-tion so that they occur only at specific parts of a molecule. By performing stepwise transforma-tions on individual chemical groups, a product can be prepared that has a controlled compo-sition and structure that are clearly related to those of the starting compound.

    But nearly all complex metal oxides are prepared at high temperatures (typically greater than 1,000 C). This is because no sol-vent is used to aid diffusion, yet the reacting ions must travel large distances (of the order of micro metres) to form the products. At these tem peratures, enough energy is avail-able to allow the occurrence of reactions that have high energy barriers. Given a choice of reaction pathways, the most favourable one is that which yields the most thermodynami-cally stable configuration of atoms. In such

    thermodynamically controlled systems, the product generally does not conserve any of the structural features of the reactants (unlike reac-tions in solution), and it is therefore much more difficult to direct the course of the reaction5.

    Tsujimoto et al.1 overcome these limitations in their preparation of SrFeO2. Their starting material is a complex metal oxide that contains Fe4+ ions (SrFeO3x, where x is about 0.125). The authors form their unusual product by remov-ing an oxide ion from the starting material, a process that is coupled to a redox reaction in which Fe4+ ions are converted into Fe2+ ions.

    The overall process uses a recently dis-covered reagent (calcium hydride) for the kinetically controlled removal of oxygen from oxides6, and it occurs at the remarkably low temperature of 280 C. These conditions pro-vide insufficient thermal energy to rearrange the structure of the starting material com-pletely only the relatively mobile oxide ions can change position (Fig. 1). The strontium and iron ions in the product retain the positions they held in the starting material. The most thermodynamically stable products iron metal and strontium(II) oxide do not form, because the required long-range diffusion for the process is too slow at this temperature. The less stable SrFeO2 forms instead, because this is a faster reaction.

    Nevertheless, the reaction pathway that

    Figure 1 | Ion movement in a complex metal oxide. Tsujimoto et al.1 report the preparation of SrFeO2 (Sr is strontium, Fe is iron), a complex metal oxide with an unusual arrangement of ions. a, The starting material (SrFeO3x, where x is about 0.125) contains FeO6 octahedra. On heating with calcium hydride, some of the oxygen ions (known as oxide ions) are lost, so that intermediate FeO4 tetrahedra form. One of the remaining oxide ions then moves to a vacant site left behind by an ion (indicated by the arrow), forming an FeO4 square. b, The crystal lattice of the starting material is an array of FeO6 octahedra, in which each oxygen is shared between two iron atoms. Strontium ions (Sr2+) fit in between the rows of octahedra. In the first step of the reaction, loss of some of the oxide ions leads to an intermediate compound, Sr2Fe2O5, consisting of alternating rows of FeO6 octahedra and FeO4 tetrahedra. In the second step, more oxide ions are lost and some of the remaining oxide ions change position. The SrFeO2 product thus forms as sheets of FeO4 squares, interleaved with strontium ions. The iron and strontium ions retain their positions throughout the process.

    a

    b

    Calciumhydride

    Starting material

    Sr2+ ions

    Intermediate Product

    280 C 280 C

    Calciumhydride

    Calciumhydride

    Calciumhydride

    280 C 280 C

    OxygenIron Vacant site

    SrFeO3x SrFeO2Sr2Fe2O5

    FeO4 tetrahedronFeO6 octahedron FeO4 square

    Corrections

    The News & Views article Venus: Express dispatches by Andrew P. Ingersoll (Nature 450, 617618; 2007) contained the erroneous statement that Venuss equator is warmer than the poles at altitudes above 65 km. It is colder.

    There was an incorrect reference citation in the article Microscopy: Elementary resolution by Christian Colliex (Nature 450, 622623; 2007). In the statement The first experimental maps are now demonstrating the importance of refining descriptions of electronmatter interactions2, the correct citation is not reference 2 but reference 12 (M. Bosman et al. Phys. Rev. Lett. 99, 086102; 2007).

    In the article Astronomy: Sloan at five by Robert C. Kennicutt Jr (Nature 450, 488489; 2007), we should clarify that the Sloan Digital Sky Survey was used only to select candidate stars for the spectroscopic observations that led to the discovery cited in reference 9 (W. R. Brown et al. Astrophys. J. 622, L33L36; 2005).

    leads to SrFeO2 (Fig. 1) is unexpected. An inter mediate (Sr2Fe2O5) is formed first, as oxide ions are removed from the starting material. This intermediate consists of alternating sheets of FeO4 tetrahedra and FeO6 octahedra. Con-version of the tetrahedra into the square planes of the final product requires that the oxide sites vacated in the formation of the intermediate be refilled with other oxide ligands. This is a crucial observation, because it demonstrates that all the oxide ions are mobile, not just those being removed from the system.

    The discovery that oxide ions can be mobile at relatively low temperatures, albeit in the presence of a strong chemical driving force, opens up a host of synthetic possibilities for example, the strong magnetic interactions seen in SrFeO2 could be modified in a controlled way by making complex oxides of different transition metals. But the practical applications are just as exciting high oxide-ion mobil-ity is required for several emerging technolo-gies, most notably solid-oxide fuel cells7. So although Tsujimoto and colleagues discovery1 may occur only at an atomic level, its ramifica-tions could extend far more widely. Michael A. Hayward is in the Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK. Matthew J. Rosseinsky is in the Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK.e-mails: [email protected];[email protected]

    1. Tsujimoto, Y. et al. Nature 450, 10621065 (2007).2. Blundell, S. Magnetism in Condensed Matter (Oxford Univ.

    Press, 2001).3. Rao, C. N. R. & Raveau, B. Transition Metal Oxides: Structure,

    Properties, and Synthesis of Ceramic Oxides 2nd edn (Wiley-VCH, Weinheim, 1998).

    4. Cava, R. J. J. Am. Ceramic Soc. 83, 528 (2000).5. Stein, A., Keller, S. W. & Mallouk, T. E. Science 259,

    15581564 (1993).6. Hayward, M. A. et al. Science 295, 18821884 (2002).7. Atkinson, A. et al. Nature Mater. 3, 1727 (2004).

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