Abstract
To accompany the Focus on Chromatin appearing in this issue of Nature Structural & Molecular Biology, a series of primers has been specially prepared that covers the wealth of knowledge in four areas of chromatin research. These areas include functions associated with covalent histone modifications, the enzymes that mediate these modifications, modules that recognize chromatin, and the ATP-dependent chromatin-remodeling complexes. In such a complex field, the information has inevitably been somewhat simplified. As an example, the correlation between modifications and functions are often context dependent. For instance, H3K9 methylation has been associated with transcriptional activation when present in the coding region of the gene, but has also been associated with repression. The reference list provides further reading and details, as do the Reviews and Perspective in this issue. Although there are many informative structures in this field, space constraints allowed only representative structures to be shown, followed by reference citations for related structures ('3D REF' column). The primers can be used as a stand-alone resource — feel free to tear them out of the issue or print out the PDF versions and modify or add to them yourself as new data emerge. The online versions of the primers contain hyperlinks to the Protein Data Bank as well as 3D view links that allow structural visualization.
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References
Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Nature 389, 251–260 (1997).
Lin, Y., Fletcher, C.M., Zhou, J., Allis, C.D. & Wagner, G. Nature 400, 86–89 (1999).
Trievel, R.C. et al. Proc. Natl. Acad. Sci. USA 96, 8931–8936 (1999).
Rojas, J.R. et al. Nature 401, 93–98 (1999).
Owen, D.J. et al. EMBO J. 19, 6141–6149 (2000).
Hudson, B.P., Martinez-Yamout, M.A., Dyson, H.J. & Wright, P.E. J. Mol. Biol. 304, 355–370 (2000).
Clements, A. et al. Mol. Cell 12, 461–473 (2003).
Poux, A.N. & Marmorstein, R. Biochemistry 42, 14366–14374 (2003).
Schuetz, A. et al. Proteins 68, 403–407 (2007).
Dhalluin, C. et al. Nature 399, 491–496 (1999).
Clements, A. et al. EMBO J. 18, 3521–3532 (1999).
Angus-Hill, M.L., Dutnall, R.N., Tafrov, S.T., Sternglanz, R. & Ramakrishnan, V. J. Mol. Biol. 294, 1311–1325 (1999).
Dutnall, R.N., Tafrov, S.T., Sternglanz, R. & Ramakrishnan, V. Cell 94, 427–438 (1998).
Yan, Y., Harper, S., Speicher, D.W. & Marmorstein, R. Nat. Struct. Biol. 9, 862–869 (2002).
Yan, Y., Barlev, N.A., Haley, R.H., Berger, S.L. & Marmorstein, R. Mol. Cell 6, 1195–1205 (2000).
Holbert M.A. et al. J Biol. Chem. published online, doi: 10.1074/jbc.M705812200 (9 October 2007).
Nielsen, P.R. et al. J. Biol. Chem. 280, 32326–32331 (2005).
Jacobson, R.H., Ladurner, A.G., King, D.S. & Tjian, R. Science 288, 1422–1425 (2000).
Somoza, J.R. et al. Structure 12, 1325–1334 (2004).
Vannini, A. et al. Proc. Natl. Acad. Sci. USA 101, 15064–15069 (2004).
Vannini, A. et al. EMBO Rep. 8, 879–884 (2007).
Min, J., Landry, J., Sternglanz, J. & Xu, R.M. Cell 105, 269–279 (2001).
Zhao, K., Chai, X., Clements, A. & Marmorstein, R. Nat. Struct. Biol. 10, 864–871 (2003).
Zhao, K., Chai, X. & Marmorstein, R. Structure 11, 1403–1411 (2003).
Zhao, K., Harshaw, R., Chai, X. & Marmorstein, R. Proc. Natl. Acad. Sci. USA 101, 8563–8568 (2004).
Sanders, B.D., Zhao, K., Slama, J.T. & Marmorstein, R. Mol. Cell 25, 463–472 (2007).
Finnin, M.S., Donigian, J.R. & Pavletich, N.P. Nat. Struct. Biol. 8, 621–625 (2001).
Hodawadekar, S.C. & Marmorstein, R. Oncogene 26, 5528–5540 (2007).
Tresaugues, L. et al. J. Mol. Biol. 359, 1170–1181 (2006).
Allen, M.D. et al. EMBO J. 25, 4503–4512 (2006).
Zhang, X. et al. Cell 111, 117–127 (2002).
Zhang, X. et al. Mol. Cell 12, 177–185 (2003).
Horita, D.A., Ivanova, A.V., Altieri, A.S., Klar, A.J. & Byrd, R.A. J. Mol. Biol. 307, 861–870 (2001).
Min, J., Zhang, X., Cheng, X., Grewal, S.I. & Xu, R.M. Nat. Struct. Biol. 9, 828–832 (2002).
Li, M. et al. Proc. Natl. Acad. Sci. USA 102, 17636–17641 (2005).
Vojnic, E., Simon, B., Strahl, B.D., Sattler, M. & Cramer, P. J. Biol. Chem. 281, 13–15 (2006).
Wilson, J.R. et al. Cell 111, 105–115 (2002).
Jacobs, S.A. et al. Nat. Struct. Biol. 9, 833–838 (2002).
Kwon, T. et al. EMBO J. 22, 292–303 (2003).
Xiao, B. et al. Nature 421, 652–656 (2003).
Couture, J-F., Collazo, E., Hauk, G. & Trievel, R.C. Nat. Struct. Mol. Biol. 13, 140–146 (2006).
Xiao, B. et al. Genes Dev. 19, 1444–1454 (2005).
Couture, J-F., Collazo, E., Brunzelle, J.S. & Trievel, R.C. Genes Dev. 19, 1455–1465 (2005).
Min, J., Feng, Q., Li, Z., Zhang, Y. & Xu, R.M. Cell 112, 711–723 (2003).
Sawada, K. et al. J. Biol. Chem. 279, 43296–43306 (2004).
Yue, W.W., Hassler, M., Roe, S.M., Thompson-Vale, V. & Pearl, L.H. EMBO J. 26, 4402–4412 (2007).
Troffer-Charlier, N., Cura, V., Hassenboehler, P., Moras, D. & Cavarelli, J. EMBO J. 26, 4391–4401 (2007).
Zhang, X. & Cheng, X. Structure 11, 509–520 (2003).
Weiss, V.H. et al. Nat. Struct. Biol. 7, 1165–1171 (2000).
Stavropoulos, P., Blobel, G. & Hoelz, A. Nat. Struct. Mol. Biol. 13, 626–632 (2006).
Yang, M. et al. Mol. Cell 23, 377–387 (2006).
Chen, Y. et al. Proc. Natl. Acad. Sci. USA 103, 13956–13961 (2006).
Yang, M. et al. Nat. Struct. Mol. Biol. 14, 535–539 (2007).
Forneris, F., Binda, C., Adamo, A., Battaglioli, E. & Mattevi, A. J. Biol. Chem. 282, 20070–20074 (2007).
Huang, Y., Fang, J., Bedford, M.T., Zhang, Y. & Xu, R.M. Science 312, 748–751 (2006).
Chen, Z. et al. Cell 125, 691–702 (2006).
Couture, J.F., Collazo, E., Ortiz-Tello, P.A., Brunzelle, J.S. & Trievel, R.C. Nat. Struct. Mol. Biol. 14, 689–695 (2007).
Chen, Z. et al. Proc. Natl. Acad. Sci. USA 104, 10818–10823 (2007).
Ng, S.S. et al. Nature 448, 87–91 (2007).
Buchwald, G. et al. EMBO J. 25, 2465–2474 (2006).
Li, Z. et al. J. Biol. Chem. 281, 20643–20649 (2006).
Worthylake, D.K., Prakash, S., Prakash, L. & Hill, C.P. J. Biol. Chem. 273, 6271–6276 (1998).
Smith, K.J. et al. Structure 12, 1067–1077 (2004).
Amodeo, G.A., Rudolph, M.J. & Tong, L. Nature 449, 492–495 (2007).
Rudolph, M.J., Amodeo, G.A., Bai, Y. & Tong, L. Biochem. Biophys. Res. Commun. 337, 1224–1228 (2005).
Nayak, V. et al. Structure 14, 477–485 (2006).
Arita, K. et al. Nat. Struct. Mol. Biol. 11, 777–783 (2004).
Arita, K. et al. Proc. Natl. Acad. Sci. USA 103, 5291–5296 (2006).
Shen, W. et al. Biochemistry 46, 2100–2110 (2007).
Singh, M., Popowicz, G.M., Krajewski, M. & Holak, T.A. ChemBioChem 8, 1308–1316 (2007).
VanDemark, A.P. et al. Mol. Cell 27, 817–828 (2007).
Jacobs, S.A. & Khorasanizadeh, S. Science 295, 2080–2083 (2002).
Nielsen, P.R. et al. Nature 416, 103–107 (2002).
Fischle, W. et al. Genes Dev. 17, 1870–1881 (2003).
Min, J., Zhang, Y. & Xu, R.M. Genes Dev. 17, 1823–1828 (2003).
Flanagan, J.F. et al. Nature 438, 1181–1185 (2005).
Zhang, P. et al. Nucleic Acids Res. 34, 6621–6628 (2006).
Lan, F. Nature 448, 718–722 (2007).
Taverna, S.D. et al. Mol. Cell 24, 785–796 (2006).
Pena, P.V. et al. Nature 442, 100–103 (2006).
Li, H. et al. Nature 442, 91–95 (2006).
Botuyan, M.V. et al. Cell 127, 1361–1373 (2006).
Couture, J.F., Collazo, E. & Trievel, R.C. Nat. Struct. Mol. Biol. 13, 698–703 (2006).
Ruthenburg, A.J. et al. Nat. Struct. Mol. Biol. 13, 704–712 (2006).
Schuetz, A. et al. EMBO J. 25, 4245–4252 (2006).
Stucki, M. et al. Cell 123, 1213–1226 (2005).
Lee, M.S., Edwards, R.A., Thede, G.L. & Glover, J.N. J. Biol. Chem. 280, 32053–32056 (2005).
Macdonald, N. et al. Mol. Cell 20, 199–211 (2005).
Wang, W.K. et al. Structure 11, 775–789 (2003).
Sathyamurthy, A., Allen, M.D., Murzin, A.G. & Bycroft, M. J. Biol. Chem. 278, 46968–46973 (2003).
Smith, C.L. et al. Nat. Struct. Biol. 10, 141–145 (2003).
Leschziner, A.E., Lemon, B., Tjian, R. & Nogales, E. Structure 13, 267–275 (2005).
Asturias, F.J., Chung, W.H., Kornberg, R.D. & Lorch, Y. Proc. Natl. Acad. Sci. USA 99, 13477–13480 (2002).
Leschziner, A.E. et al. Proc. Natl. Acad. Sci. USA 104, 4913–4918 (2007).
Skiniotis, G., Moazed, D. & Walz, T. J. Biol. Chem. 282, 20804–20808 (2007).
Da, G. et al. Proc. Natl. Acad. Sci. USA 103, 2057–2062 (2006).
Dürr, H., Koerner, C., Mueller, M., Hickmann, V. & Hopfner, K.P. Cell 121, 363–373 (2005).
Bowman, B.R. et al. Structure 14, 151–158 (2006).
Zhang, P. et al. Protein Sci. 15, 2423–2434 (2006).
Matias, P.M., Gorynia, S., Donner, P. & Carrondo, M.A. J. Biol. Chem. 281, 38918–38929 (2006).
Okuda, M., Horikoshi, M. & Nishimura, Y. J. Mol. Biol. 365, 1047–1062 (2007).
Flanagan, J.F. et al. J. Mol. Biol. 369, 334–342 (2007).
Grune, T. et al. Mol. Cell 12, 449–460 (2003).
Horton, J.R. et al. Proteins 67, 1198–1202 (2007).
Hartlepp, K.F. et al. Mol. Cell. Biol. 25, 9886–9896 (2005).
Allis, C. D, Jenuwein, T. & Reinberg, D. Epigenetics (eds. Allis, C.D., Jenuwein, T. & Reinberg, D.) Appendix 2 (Cold Spring Harbor Press, Cold Spring Harbor, New York, USA, 2007).
Bhaumik, S., Smith, E. & Shilatifard, A. Nat. Struct. Mol. Biol. 14, 1006–1016 (2007).
Taverna, S.D., Li, H., Ruthenburg, A., Allis, C.D. & Patel, D.J. Nat. Struct. Mol. Biol. 14, 1025–1040 (2007).
Latham, J. & Dent, S.Y. Nat. Struct. Mol. Biol. 14, 1017–1024 (2007).
Buhler, M. & Moazed, D. Nat. Struct. Mol. Biol. 14, 1041–1048 (2007).
De Koning, L. et al. Nat. Struct. Mol. Biol. 14, 997–1007 (2007).
Sexton, T., Schober, H., Fraser, P. & Gasser, S. Nat. Struct. Mol. Biol. 14, 1049–1055 (2007).
Barski, A. et al. Cell 129, 823–837 (2007).
Kouzarides, T. Cell 128, 693–705 (2007).
Li, B., Carey, M. & Workman, J.L. Cell 128, 707–719 (2007).
Berger, S.L. Nature 447, 407–412 (2007).
Mersfelder, E.L. & Parthun, M.R. Nucleic Acids Res. 34, 2653–2662 (2006).
Hassa, P.O., Haenni, S.S., Elser, M. & Hottiger, M.O. Microbiol. Mol. Biol. Rev. 70, 789–829 (2006).
Martin, C. & Zhang, Y. Nat. Rev. Mol. Cell Biol. 6, 838–849 (2005).
Nowak, S.J. & Corces, V.G. Trends Genet. 20, 214–220 (2004).
Jenuwein, T. & Allis, C.D. Science 293, 1074–1080 (2001).
Zhang, Y. & Reinberg, D. Genes Dev. 15, 2343–2360 (2001).
Strahl, B.D. & Allis, C.D. Nature 403, 41–45 (2000).
Shi, Y. & Whetstine, J.R. Mol. Cell 25, 1–14 (2007).
Couture, J.F. & Trievel, R.C. Curr. Opin. Struct. Biol. 16, 753–760 (2006).
Dillon, S.C., Zhang, X., Trievel, R.C. & Cheng, X. Genome Biol. 6, 227 (2005).
Holbert, M.A. & Marmorstein, R. Curr. Opin. Struct. Biol. 15, 673–680 (2005).
Sterner, D.E. & Berger, S.L. Microbiol. Mol. Biol. Rev. 64, 435–459 (2000).
Kim, J. et al. EMBO Rep. 7, 397–403 (2006).
Bottomley, M.J. EMBO Rep. 5, 464–469 (2004).
Chen, M. & Shen, X. Curr. Opin. Cell Biol. 19, 326–330 (2007).
Bao, Y. & Shen, X. Mutat. Res. 618, 18–29 (2007).
Denslow, S.A. & Wade, P.A. Oncogene 26, 5433–5438 (2007).
Moshkin, Y.M., Mohrmann, L., van Ijcken, W.F. & Verrijzer, C.P. Mol. Cell. Biol. 27, 651–661 (2007).
Varga-Weisz, P.D. & Becker, P.B. Curr. Opin. Genet. Dev. 16, 151–156 (2006).
Cairns, B.R. Curr. Opin. Genet. Dev. 15, 185–190 (2005).
Eberharter, A. & Becker, P.B. J. Cell Sci. 117, 3707–3711 (2004).
Lessard, J. et al. Neuron 55, 201–215 (2007).
Becker, P.B. & Horz, W. Annu. Rev. Biochem. 71, 247–273 (2002).
Mujtaba, S. et al. Mol. Cell 13, 251–263 (2004).
Han, Z. et al. Mol. Cell 22, 137–144 (2006).
Acknowledgements
Thank you to the people that gave us feedback at different stages, including Francisco J. Asturias, Geneviève Almouzni, Peter B. Becker, Mark T. Bedford, Dan Bochar, Karim Bouazoune, Bradley R. Cairns, Joan A. Conaway, Jacques Côté, Gerald R. Crabtree, Yali Dou, Anindya Dutta, Michael Grunstein, Thomas Jenuwein, Tony Kouzarides, Robert E. Kingston, Sepideh Khorasanizadeh, Ronen Marmorstein, Georges Mer, Jane Mellor, Mary Ann Osley, Tom Owen-Hughes, Craig L. Peterson, Geeta Narlikar, Toshio Tsukiyama, Xuetong Shen, Yang Shi, Ali Shilatifard, Song Tan, Sean D. Taverna, Raymond C. Trievel, Patrick Varga-Weisz, C. Peter Verrijzer and Paul Wade. Cover by Erin Boyle, based on “Crosstalk” by Colleen Buzzard (http://www.colleenbuzzard.com).
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Lall, S. Primers on chromatin. Nat Struct Mol Biol 14, 1110–1115 (2007). https://doi.org/10.1038/nsmb1107-1110
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DOI: https://doi.org/10.1038/nsmb1107-1110
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