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To the Editor: abcd Centromeres are specialized segments of chro- mosomes that aid in chromosomal segrega- tion after DNA replication. The kinetochore is a protein complex that interacts specifically with the centromere to allow the separation of sister chromosomes into the daughter cells. If the centromere becomes damaged or removed, the chromosomes segregate randomly. This Figure 1 The models of nucleosomes and nucleosomal arrays, projected on a plane. (a–d) Schematic suggests that centromeres contain specific structures of H3 and CENP-A mononucleosomes (a and b, respectively) and their arrangements into characteristics that allow their selection by arrays (c and d, respectively). Histone cores are shown as yellow and green disks. kinetochores. However, the structural details of centromeres and the mechanism underlying this can be used to generate models for nucleosome systems. In this respect, it might be attractive recognition process remain unclear. It is known arrangements for both types of nucleosomes. to consider high-speed AFM, which is capable that all centromeric nucleosomes contain modi- The flanking DNA sequences emerging from of visualizing structural features at nanometer fied H3 histones (CENP-A; reviewed in ref. 1). H3 nucleosomes cross each other at an ~90° resolution and which was successfully used to An analysis of the CENP-A–­nucleosome array angle (Fig. 1a), whereas in CENP-A nucleo- study the dynamics of mononucleosomes9. by atomic force microscopy (AFM) revealed somes the flanking sequences are nearly par- Nature America, Inc. All rights reserved. America, Inc. © 201 4 Nature that CENP-A nucleosomes have a considerably allel (~0°) because the wrapped DNA is 26 bp ACKNOWLEDGMENTS 2 This work was supported by US National Institutes of lower height than do regular H3 nucleosomes . shorter (Fig. 1b). This arrangement generates Health grant 5R01GM100156. The authors therefore suggested that CENP-A the well-known zig-zag model for H3 nucleo- npg nucleosomes consist of one set of each histone somes (Fig. 1c), whereas CENP-A nucleosomes COMPETING FINANCIAL INTERESTS (tetrasome) rather than the histone duplicates form a parallel array (Fig. 1d). The possibility The author declares no competing financial interests. observed in regular H3 nucleosomes (octa- that these nucleosomal arrangements lead to Yuri L Lyubchenko somes). However, s­ubsequent crystallographic different higher-order structures of centromeric data did not confirm this finding3, revealing and regular chromatin is a crucial question that Department of Pharmaceutical Sciences, instead that both types of nucleosomes are needs to be addressed in future studies. University of Nebraska Medical Center, octameric. The c­ontroversy was reconciled in At present, however, additional issues need Omaha, Nebraska, USA. a recent ­publication by Miell et al.4 in which to be considered. Two recent reports6,7 chal- e-mail: [email protected] a thorough AFM analysis was combined with lenge the finding that CENP-A nucleosomes 1. Henikoff, S. & Dalal, Y. Curr. Opin. Genet. Dev. 15, biochemical tests, showing that CENP-A have reduced heights because their analy- 177–184 (2005). 6 7 nucleosomes had a lower height than did H3 sis of mononucleosomes and arrays made 2. Dalal, Y., Wang, H., Lindsay, S. & Henikoff, S. PLoS nucleosomes and that both were octameric with both types of H3 histones did not reveal Biol. 5, e218 (2007). 4 3. Tachiwana, H., Kagawa, W. & Kurumizaka, H. Nucleus particles. Miell et al. s­uggest that CENP-A a height difference. These studies and the 3, 6–11 (2012). nucleosomes are s­ tructurally dif­ ferent from H3 response by Miell et al.8 provide a number of 4. Miell, M.D. et al. Nat. Struct. Mol. Biol. 20, 763–765 nucleosomes, and this conclusion is in agree- explanations for these differences, including (2013). 5. Shlyakhtenko, L.S., Lushnikov, A.Y. & Lyubchenko, Y.L. ment with cr­ ystallographic models for both experimental problems related to use of AFM. Biochemistry 48, 7842–7848 (2009). types of nucleosomes3. Indeed, terminal DNA The data reported by Miell et al.4,8 imply that 6. Walkiewicz, M.P., Dimitriadis, E.K. & Dalal, Y. Nat. Struct. Mol. Biol. 21, 2–3 (2014). segments of CENP-A nucleosomes (13 bp) are CENP-A nucleosomes are more dynamic than 7. Codomo, C.A., Furuyama, T. & Henikoff, S. Nat. Struct. detached from the histone core, and this partial H3 nucleosomes. To validate this claim, struc- Mol. Biol. 21, 4–5 (2014). unwrapping decreases the volume and hence tural studies should be combined with single- 8. Miell, M.D., Straight, A.F. & Allshire, R.C. Nat. Struct. 5 Mol. Biol. 21, 5–8 (2014). the height of the nucleosome . The crystallo- molecule biophysics approaches capable of 9. Miyagi, A., Ando, T. & Lyubchenko, Y.L. Biochemistry graphic data for CENP-A and H3 nucleosomes3 characterizing dynamic states of biological 50, 7901–7908 (2011).

8 volume 21 number 1 JANUARY 2014 nature structural & molecular biology