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Pol ε Leading strand
Okazaki fragment
Nucleosome Lagging strand Pol δ
Figure 1 | Asymmetric DNA replication. The sequences of the two strands of a DNA molecule run in opposite directions, but during replication the new DNA molecules are synthesized in only one direction. Each strand is therefore duplicated differently. The leading strand is used as a template by a polymerase enzyme (Pol ε, top), which makes a new molecule in a continuous manner. By contrast, duplication of the lagging strand is discontinuous and requires another polymerase (Pol δ, bottom), which synthesizes short DNA pieces known as Okazaki fragments. These fragments are then joined together with the help of other enzymes to form a continuous molecule. During the process, nucleosomes — protein complexes around which DNA is coiled — disassemble from parental DNA to then reassemble, along with additional nucleosome proteins as needed, allowing both DNA duplication and chromatin reorganization. Smith and Whitehouse’s analysis2 of Okazaki fragments illuminates the link between nucleosome assembly and the synthesis of the lagging strand.
was long enough, and then the next fragment would be synthesized. This assumption tallies with the observation that the average length of Okazaki fragments is similar to that of the DNA wound around a nucleosome. The authors2 propose an alternative model in which the presence of a nascent nucleosome acts as a roadblock to an advancing polymerase enzyme (Pol δ), which is synthesizing the lagging strand. According to their model, Pol δ and other associated enzymes can invade the nascent nucleosome up to its dyad axis, but then the nucleosome mediates the dissociation of all of these enzymes from the DNA — by doing so, the nucleosome determines the length of the Okazaki fragment. To test the model, Smith and Whitehouse used yeast strains in which the physiological balance between polymerases and nucleo somes was altered, either because the polymerases were less active or because nucleosome assembly was impaired. For example, they observed2 that the Okazaki fragments were longer in mutant strains defective in CAF-1, a protein complex known5 to act as a histone chaperone, which promotes histone deposition on newly synthesized DNA. Therefore, the tight balance between the capacity to form a new nucleosome on the lagging strand and the polymerase’s ability to advance is what sets the length of the Okazaki fragment. These findings also suggest that the efficiency of the replication machinery’s progression may depend on where the nucleosome forms. The authors’ work provides the basis for research on how other factors involved in histone dynamics and nucleosome movement on DNA — such as histone chaperones5 and chromatin remodeller enzymes — can affect Okazaki-fragment size and, overall, DNA
replication. Moreover, additional proteins involved in chromatin assembly could be identified by screening the available collection of yeast mutants for changes in Okazakifragment length. And the technique used for mapping Okazaki fragments offers a means to identify the genomic sites at which DNA replication starts. It is tempting to postulate that the inherent asymmetry of nucleosome dynamics during DNA replication could contribute to
a mechanism for asymmetric cell division, a process by which two different cell types are generated. This hypothesis is supported by the finding6 that CAF-1 has a role in asymmetric cell division in the worm Caenorhabditis elegans. In addition, histones in nucleosomes exist in different forms associated with specific genomic regions, and can be ‘marked’ with various chemical modifications that reflect functional states, such as activation or repression of gene expression. Whereas some of these modifications are transient, others may be inherited during cell division in an epigenetic fashion — that is, independently of the DNA sequence. But to understand how the chemical modifications of nucleosomes can be inherited during cell division, we must first determine how nucleosomal organization is reproduced during DNA replication. So Smith and Whitehouse’s study paves the way for a deeper exploration of the intimate relationship between genetics and epigenetics. ■ Alysia Vandenberg and Geneviève Almouzni are in Unit UMR218, Institut Curie/Centre National de la Recherche Scientifique, Paris F-75248, France. e-mail:
[email protected] 1. Saha, A., Wittmeyer, J. & Cairns, B. R. Nature Rev. Mol. Cell Biol. 7, 437–447 (2006). 2. Smith, D. J. & Whitehouse, I. Nature 483, 434–438 (2012). 3. Jiang, C. & Pugh, B. F. Genome Biol. 10, R109 (2009). 4. Anderson, S. & DePamphilis, M. L. J. Biol. Chem. 254, 11495–11504 (1979). 5. Corpet, A. & Almouzni, G. Trends Cell Biol. 19, 29–41 (2009). 6. Nakano, S., Stillman, B. & Horvitz, H. R. Cell 147, 1525–1536 (2011).
GEO C H EM I ST RY
Bubbles from the deep A study suggests that hydrocarbons released from sedimentary basins formed part of a climatic feedback mechanism that exacerbated global warming during the Eocene epoch. HENRIK SVENSEN
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as released from sedimentary basins has been proposed to be a key player in many of the rapid climate changes that occurred in the past 250 million years. The types and sources of the released gases are still debated, but they probably included gases formed by the heating of organic matter around hot magma1, and gases released by the dissociation of gas hydrates (solid compounds that trap gas molecules) found in deep-ocean sediments2. The influence of hydrates is greater in a warming world because higher ocean temperatures can melt methane-bearing gas hydrates, releasing the gas. The methane can
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then be oxidized to carbon dioxide, causing ocean acidification, and can contribute to global warming because both methane and carbon dioxide are greenhouse gases. Writing in Geophysical Research Letters, Kroeger and Funnell3 suggest another way in which global warming can lead to increased gas emissions from the sea floor. Sedimentary basins have large accumulations of biological, inorganic and clastic deposits (which consist of fragments of pre-existing rocks), and are host to more than 99.9% of the organic carbon in Earth’s crust. This amounts to a staggering 15,000,000 gigatonnes (Gt) of carbon; for comparison, 3,300 Gt of carbon are stored in all known hydrocarbon and
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Hyperthermals PETM
12 Ocean temperature (°C)
coal reserves4. Any viable mechanism for transferring significant quantities of sedimentbound carbon to the atmosphere on a short timescale may thus perturb the global carbon cycle and lead to global warming. A series of such perturbations has been suggested5,6 to have happened in the Eocene epoch (which ran from 55.8 million to 33.9 million years ago) to explain several short-lived climatic anomalies that occurred during a period of otherwise steady warming from 58 to 50 Myr ago (Fig. 1). The most prominent of these events was the Palaeocene–Eocene thermal maximum (PETM), which was characterized by global warming of 5–10 °C and subtropical conditions in the Arctic. One cause of the PETM is commonly assumed to have been methane release to the atmosphere that was triggered either by the melting of gas hydrates2 or by the heating of rocks rich in organic material in sedimentary basins (caused by widespread volcanic activity in the northeast Atlantic region1,7). The extended period of warming during the Eocene culminated in the Early Eocene Climatic Optimum (EECO) 52 to 50 Myr ago, the hottest prolonged climatic episode since the Cretaceous period 145.5 to 65.5 Myr ago. Kroeger and Funnell3 focus on the EECO in their work. Using computer models of four sedimentary basins in the southwest Pacific, they simulated the increase in hydrocarbon generation in the basins as the warming Eocene oceans transferred heat to the sea floor and to deep-seated, organic-rich rocks. The sedimentary basins studied by the authors all contained rocks that could produce petroleum given the right temperature conditions and sufficient time. Organic matter within the sedimentary rocks can convert into petroleum at temperatures of 60–120 °C (the oil window), or into predominantly natural gas at temperatures of 100–200 °C (the gas window). On the basis of their models, Kroeger and Funnell estimate that the warming ocean during and after the PETM eventually raised the temperature of a 300-metre-thick layer of sediments into the oil and gas windows. A marked rise in hydrocarbon production would therefore have occurred in the 4 to 5 Myr following the PETM, peaking during the EECO. The authors’ results help us to understand the dynamics and temperature-dependence of hydrocarbon (petroleum and gas) generation in sedimentary basins. But there is more to the story than that. If oil and gas generated during the Eocene somehow escaped the sedimentary basins and leaked out to the ocean and the atmosphere in sufficient quantities, this may have contributed to global warming at the time. In other words, Kroeger and Funnell propose a climate feedback mechanism: global warming causes increased hydrocarbon production that leads to prolonged global warming.
10
8
EECO Palaeocene 60
Eocene 55.8
50
Time (million years ago)
Figure 1 | Ancient climate change. The graph depicts ocean temperatures during the Palaeocene and early Eocene epochs, estimated from the abundance of oxygen isotopes in microfossils5,6. A warming trend from about 58 to 50 Myr ago was punctuated by short-lived climatic anomalies known as hyperthermals, of which the Palaeocene–Eocene Thermal Maximum (PETM) was the greatest. The warmest climate occurred during the Early Eocene Climatic Optimum (EECO) about 52 to 50 Myr ago, after which climate cooling occurred. The PETM may have been caused in part by the release of methane to the atmosphere, triggered by the melting of gas hydrates (solids that trap gases in ocean sediments) and/or by the heating of organic matter by intruding magma in sedimentary basins. Kroeger and Funnell3 propose that the production of hydrocarbons (petroleum and natural gas) in sedimentary basins increased during and after the PETM, and that seepage of hydrocarbons from such basins into the ocean and atmosphere contributed to global warming.
The idea that the conversion of organic matter into petroleum following a temperature increase in sedimentary basins may form part of a climate feedback mechanism was first posited8 by Kroeger and colleagues last year. The modelling in Kroeger and Funnell’s present work3 remarkably predicts and quantifies a peak in hydrocarbon production that overlaps in time with the EECO. The authors’ results show that about 37 Gt of oil and 8 Gt of gas were generated from the four basins during this period, which is 50% more than would have occurred in the absence of extra ocean warming. This alone would not have been sufficient to affect the Eocene climate9, but many other basins around the world would presumably have increased in temperature at the same time. The mass of hydrocarbons generated globally could therefore have been considerably higher than that predicted in the authors’ study, although the exact amount is difficult to quantify. Is hydrocarbon seepage at the sea floor on a climate-changing scale a realistic possibility? Kroeger and Funnell argue that it is, because more oil and gas are generated in sedimentary basins than are trapped10. Studies11 of sedimentary basins around the globe have shown that gas seepage is currently a common phenom enon, and there is no reason why this should not have been the case earlier in Earth’s history12. But did the hydrocarbons predicted3 to have been generated during the Eocene really leak out to the ocean and atmosphere, or did they stay trapped in the subsurface? A way to test this is to search for carbonate deposits in old sea-floor sediments, because sea-floor hydrocarbon seepage leaves behind deposits that © 2012 Macmillan Publishers Limited. All rights reserved
have distinct geochemical signals that can be attributed to their origin13. Unfortunately, the carbonate record is currently too poorly investigated to confirm the extent of seepage from sedimentary basins during the Eocene, and so more studies are needed. Nevertheless, one thing seems clear: the transfer of carbon from sedimentary rocks to the atmosphere is an important component of climate change, both past and future. ■ Henrik Svensen is at the Centre for Physics of Geological Processes, University of Oslo, PO Box 1048, Blindern, 0316 Oslo, Norway. e-mail:
[email protected] 1. Svensen, H. et al. Nature 429, 542–545 (2004). 2. Dickens, G. R., O’Neil, J. R., Rea, D. K. & Owen, R. M. Paleoceanography 10, 965–971 (1995). 3. Kroeger, K. F. & Funnell, R. H. Geophys. Res. Lett. http://dx.doi.org/10.1029/2011GL050345 (2012). 4. www.grida.no/publications/other/ipcc_tar 5. Zachos, J. C., Pagani, M., Sloan, L., Thomas, E. & Billups, K. Science 292, 686–693 (2001). 6. Sluijs, A., Bowen, G. J., Brinkhuis, H., Lourens, L. J. & Thomas, E. in Deep Time Perspectives on Climate Change: Marrying the Signal from Computer Models and Biological Proxies (eds Williams, M., Haywood, A., Gregory, J. & Schmidt, D.) 267–293 (Geol. Soc. Lond., 2007). 7. Storey, M., Duncan, R. A. & Swisher, C. C. III Science 316, 587–589 (2007). 8. Kroeger, K. F., di Primio, R. & Horsfield, B. Earth Sci. Rev. 107, 423–442 (2011). 9. Cui, Y. et al. Nature Geosci. 4, 481–485 (2011). 10. Kvenvolden, K. A. & Cooper, C. K. Geo-Mar. Lett. 23, 140–146 (2003). 11. Serié, C. S., Huuse, M. & Schødt, N. H. Geology http://dx.doi.org/10.1130/G32690 (2012). 12. Berndt, C. Phil. Trans. R. Soc. A 363, 2855–2871 (2005). 13. Mazzini, A., Aloisi, G., Akhmanov, J., Parnell, B. & Murphy, P. J. Geol. Soc. Lond. 162, 815–827 (2005).
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