Nachrichten aus der Chemie (the membership magazine of the GDCh) annually publishes trend reports in which authors spot and compile an overview of inspiring work and recent trends in the most important chemical disciplines.

ChemViews gives you an overview of the latest trend report, its authors and the literature collected.

Trends in Biochemistry 2011

M. Helm, M. Mörl, P. F. Stadler, S. Hoffmann, C. Höbartner

• RNA: Deep sequencing is the next step in the RNA revolution.
• Epigenetics: 5-Hydroxymethylcytosine, the sixth base in the genome, is discussed as a novel epigenetic modification.

► Full article (in German):

Trendbericht Biochemie 2011,

• Deep Sequencing,
  M. Helm, M. Mörl, P. F. Stadler, S. Hoffmann,
  Nachrichten aus der Chemie 2012, 60(3), 300–307.
• 5-Hydroxymethylcytosin im Genom,
  C. Höbartner,
  Nachrichten aus der Chemie 2012, 60(3), 308–312.

► All 2011 trend reports on ChemViews

Authors

Mark Helm, born 1969, has been a Professor of Pharmaceutical/Medicinal Chemistry at the University of Mainz, Germany, since 2009. He received his Ph.D. in 1999 in molecular biology at the University of Strasbourg, France, after which he undertook postdoctoral research at the California Institute of Technology, USA, and at the Freie Universität Berlin, Germany. After that, he became a Senior Research Scientist in the Department of Chemistry at the Institute of Pharmacy and Molecular Biotechnology of the University of Heidelberg, Germany, where he obtained his Habilitatation in 2008 in the fields of pharmaceutical chemistry and biochemistry.

His research interests include ribonucleotide modification, the structural dynamics of RNA molecules, the uptake and intracellular distribution of siRNA, and RNA bioconjugates.

Mario Mörl, born 1960, studied biology at the Ludwig Maximilian University of Munich, Germany. There, he completed his Ph.D. on ribozymes before becoming a Postdoctoral Fellow and Research Assistant to S. Pääbo. In 1999, he became Group Leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He completed his Habilitation in 2002 in genetics and he has been Professor of Biochemistry and Molecular Biology at the University of Leipzig since 2004.

His research interests include the evolution of RNA-specific nucleotidyltransferases, tRNA editing events, as well as the in vitro evolution of RNA aptamers.

Peter F. Stadler, born 1965, has been a Professor of Bioinformatics at the University of Leipzig, Germany, since 2002. He received his Ph.D. in chemistry from the University of Vienna, Austria, in 1990. After a postdoctoral fellowship at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, he returned to Vienna in 1991 and received his Habilitation in theoretical chemistry in 1994. Since 1994, he has also been an External Professor at the Santa Fe Institute in New Mexico, USA, and, since 2009, he has acted as an External Scientific Member at the Max Planck Institute for Mathematics in the Sciences in Leipzig.

His research interests include bioinformatics with an emphasis on structural biology and comparative genomics, non-coding RNAs, the mathematical foundations of evolutionary biology, and discrete mathematics.

Steve Hoffmann, born 1978, is the Director of the Research Group for Transcriptome Bioinformatics in the LIFE Center for Lifestyle Diseases at the University of Leipzig, Germany. He has a doctorate in medicine and bioinformatics.

He is interested in the design of algorithms and methods for the evaluation of high-throughput data-sequencing.

Since 2008, Claudia Höbartner, born 1977, has led the Max-Planck Research Group for Nucleic Acid Chemistry at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany. She studied chemistry at the Technical University of Vienna, Austria, and at the ETH Zurich, Switzerland, and received her Ph.D. at the University of Innsbruck, Austria, in 2004. She took up a position as a Postdoctoral Fellow at the University of Illinois, Urbana-Champaign, USA.

Her research interests focus on chemically modified nucleic acids and catalytically active DNA.

References

Deep Sequencing

1) A. Mellmann, D. Harmsen, C. A. Cummings, E. B. Zentz, S. R. Leopold, A. Rico, K. Prior, R. Szczepanowski, Y. Ji, W. Zhang, S. F. McLaughlin, J. K. Henkhaus, B. Leopold, M. Bielaszewska, R. Prager, P. M. Brzoska, R. L. Moore, S. Guenther, J. M. Rothberg, H. Karch, PLoS One 2011, 6, e22751. DOI: 10.1371/journal.pone.0022751
2) S. Findeiss, D. Langenberger, P. F. Stadler, S. Hoffmann, Biol. Chem. 2011, 392, 305. DOI:10.1515/bc.2011.043
3) J. B. Lucks, S. A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G. P. Schroth, L. Pachter, J. A. Doudna, A. P. Arkin, Proc. Natl. Acad. Sci. USA 2011, 108, 11063. DOI: 10.1073/pnas.1106501108
4) C. A. Raabe, C. H. Hoe, G. Randau, J. Brosius, T. H. Tang, T. S. Rozhdestvensky, RNA 2011, 17, 1357. DOI: 10.1261/rna.2682311
5) J. M. Liu, J. Livny, M. S. Lawrence, M. D. Kimball, M. K. Waldor, A. Camilli, Nucleic Acids Res. 2009, 37, e46. DOI: 10.1093/nar/gkp080
6) M. Hafner, N. Renwick, M. Brown, A. Mihailovic, D. Holoch, C. Lin, J. T. Pena, J. D. Nusbaum, P. Morozov, J. Ludwig, T. Ojo, S. Luo, G. Schroth, T. Tuschl, RNA 2011, 17, 1697. DOI: 10.1261/rna.2799511
7) C. M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, A. Sittka, S. Chabas, K. Reiche, J. Hackermuller, R. Reinhardt, P. F. Stadler, J. Vogel, Nature 2010, 464, 250. DOI: 10.1038/nature08756
8) J. Mitschke, J. Georg, I. Scholz, C. M. Sharma, D. Dienst, J. Bantscheff, B. Voss, C. Steglich, A. Wilde, J. Vogel, W. R. Hess, Proc. Natl. Acad. Sci. USA 2011, 108, 2124. DOI: 10.1073/pnas.1015154108
9) S. Aviran, C. Trapnell, J. B. Lucks, S. A. Mortimer, S. Luo, G. P. Schroth, J. A. Doudna, A. P. Arkin, L. Pachter, Proc. Natl. Acad. Sci. USA 2011, 108, 11069. DOI: 10.1073/pnas.1106541108
10) J. N. Pitt, A. R. Ferre-D’Amare, Science 2010, 330, 376. DOI: 10.1126/science.1192001
11) C. Kluwe, A. D. Ellington, Science 2010, 330, 330. DOI: 10.1126/science.1197667
12) Nat. Biotechnol. 2008, 26, 1099. DOI: 10.1038/nbt1008-1099
13) S. V. Angiuoli, J. R. White, M. Matalka, O. White, W. F. Fricke, PLoS One 2011, 6, e26624. DOI: 10.1371/journal.pone.0026624
14) V. A. Fusaro, P. Patil, E. Gafni, D. P. Wall, P. J. Tonellato, PLoS Comput. Biol. 2011, 7, e1002147. DOI: 10.1371/journal.pcbi.1002147
15) D. Langenberger, C. I. Bermudez-Santana, P. F. Stadler, S. Hoffmann, Pac. Symp. Biocomput. 2010, 80.
16) P. J. Cock, C. J. Fields, N. Goto, M. L. Heuer, P. M. Rice, Nucleic Acids Res. 2010, 38, 1767. DOI: 10.1093/nar/gkp1137
17) S. Hoffmann, C. Otto, S. Kurtz, C. M. Sharma, P. Khaitovich, J. Vogel, P. F. Stadler, J. Hackermuller, PLoS Comput. Biol. 2009, 5, e1000502. DOI: 10.1371/journal.pcbi.1000502
18) H. Li, R. Durbin, Bioinformatics 2010, 26, 589. DOI: 10.1093/bioinformatics/btp698
19) B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, Genome Biol. 2009, 10, R25. DOI: 10.1186/gb-2009-10-3-r25
20) H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, Bioinformatics 2009, 25, 2078. DOI: 10.1093/bioinformatics/btp352
21) E. R. Mardis, Genome Med. 2010, 2, 84. DOI: 10.1186/gm205
22) K. Iida, H. Jin, J. K. Zhu, BMC Genomics 2009, 10, 155. DOI: 10.1186/1471-2164-10-155
23) H. A. Ebhardt, H. H. Tsang, D. C. Dai, Y. Liu, B. Bostan, R. P. Fahlman, Nucleic Acids Res. 2009, 37, 2461. DOI: 10.1093/nar/gkp093
24) C. Schmidtke, S. Findeiss, C. M. Sharma, J. Kuhfuss, S. Hoffmann, J. Vogel, P. F. Stadler, U. Bonas, Nucleic Acids Res. 2011. DOI: 10.1093/nar/gkr904

5-Hydroxymethylcytosine in the Genome

1) K. Keller, M. Jung, Nachr. Chem. 2011, 59, 822. DOI: 10.1002/nadc.201190014
2) S. Kriaucionis, N. Heintz, Science 2009, 324, 929. DOI: 10.1126/science.1169786
3) M. Tahiliani, K. P. Koh, Y. Shen, W. A. Pastor, H. Bandukwala, Y. Brudno, S. Agarwal, L. M. Iyer, D. R. Liu, L. Aravind, A. Rao, Science 2009, 324, 930. DOI: 10.1126/science.1170116
4) G. R. Wyatt, S. S. Cohen, Nature 1952, 170, 1072. DOI: 10.1038/1701072a0
5) M. Münzel, D. Globisch, T. Bruckl, M. Wagner, V. Welzmiller, S. Michalakis, M. Müller, M. Biel, T. Carell, Angew. Chem. 2010, 122, 5503. DOI: 10.1002/ange.201002033
6) D. Globisch, M. Münzel, M. Müller, S. Michalakis, M. Wagner, S. Koch, T. Bruckl, M. Biel, T. Carell, PLoS One 2010, 5, e15367. DOI: 10.1371/journal.pone.0015367
7) C. X. Song, K. E. Szulwach, Y. Fu, Q. Dai, C. Yi, X. Li, Y. Li, C. H. Chen, W. Zhang, X. Jian, J. Wang, L. Zhang, T. J. Looney, B. Zhang, L. A. Godley, L. M. Hicks, B. T. Lahn, P. Jin, C. He, Nat. Biotechnol. 2011, 29, 68. DOI: 10.1038/nbt.1732
8) K. E. Szulwach, X. Li, Y. Li, C. X. Song, H. Wu, Q. Dai, H. Irier, A. K. Upadhyay, M. Gearing, A. I. Levey, A. Vasanthakumar, L. A. Godley, Q. Chang, X. Cheng, C. He, P. Jin, Nat. Neurosci. 2011, 14, 1607. DOI: 10.1038/nn.2959
9) J. U. Guo, D.K. Ma, H. Mo, M. P. Ball, M. H. Jang, M. A. Bonaguidi, J. A. Balazer, H. L. Eaves, B. Xie, E. Ford, K. Zhang, G. L. Ming, Y. Gao, H. Song, Nat. Neurosci. 2011, 14, 1345. DOI: 10.1038/nn.2900
10) K. Iqbal, S. G. Jin, G. P. Pfeifer, P. E. Szabo, Proc. Natl. Acad. Sci. USA 2011, 108, 3642. DOI: 10.1073/pnas.1014033108
11) M. Wossidlo, T. Nakamura, K. Lepikhov, C. J. Marques, V. Zakhartchenko, M. Boiani, J. Arand, T. Nakano, W. Reik, J. Walter, Nat. Commun. 2011, 2, 241. DOI: 10.1038/ncomms1240
12) T. Pfaffeneder, B. Hackner, M. Truss, M. Münzel, M. Müller, C. A. Deiml, C. Hagemeier, T. Carell, Angew. Chem. 2011, 123, 7146. DOI: 10.1002/ange.201103899
13) S. Ito, L. Shen, Q. Dai, S. C. Wu, L. B. Collins, J. A. Swenberg, C. He, Y. Zhang, Science 2011, 333, 1300. DOI: 10.1126/science.1210597
14) Y. F. He, B. Z. Li, Z. Li, P. Liu, Y. Wang, Q. Tang, J. Ding, Y. Jia, Z. Chen, L. Li, Y. Sun, X. Li, Q. Dai, C. X. Song, K. Zhang, C. He, G. L. Xu, Science 2011, 333, 1303. DOI: 10.1126/science.1210944
15) A. Maiti, A. C. Drohat, J. Biol. Chem. 2011, 286, 35334. DOI: 10.1074/jbc.C111.284620
16) S. Cortellino, J. Xu, M. Sannai, R. Moore, E. Caretti, A. Cigliano, M. Le Coz, K. Devarajan, A. Wessels, D. Soprano, L. K. Abramowitz, M. S. Bartolomei, F. Rambow, M. R. Bassi, T. Bruno, M. Fanciulli, C. Renner, A. J. Klein-Szanto, Y. Matsumoto, D. Kobi, I. Davidson, C. Alberti, L. Larue, A. Bellacosa, Cell 2011, 146, 67. DOI: 10.1016/j.cell.2011.06.020
17) C. Frauer, T. Hoffmann, S. Bultmann, V. Casa, M. C. Cardoso, I. Antes, H. Leonhardt, PLoS One 2011, 6, e21306. DOI: 10.1371/journal.pone.0021306
18) G. Ficz, M. R. Branco, S. Seisenberger, F. Santos, F. Krueger, T. A. Hore, C. J. Marques, S. Andrews, W. Reik, Nature 2011, 473, 398. DOI: 10.1038/nature10008
19) A. Szwagierczak, A. Brachmann, C. S. Schmidt, S. Bultmann, H. Leonhardt, F. Spada, Nucleic Acids Res. 2011, 39, 5149. DOI: 10.1093/nar/gkr118
20) W. A. Pastor, U. J. Pape, Y. Huang, H. R. Henderson, R. Lister, M. Ko, E. M. McLoughlin, Y. Brudno, S. Mahapatra, P. Kapranov, M. Tahiliani, G. Q. Daley, X. S. Liu, J. R. Ecker, P. M. Milos, S. Agarwal, A. Rao, Nature 2011, 473, 394. DOI: 10.1038/nature10102
21) C. X. Song, T. A. Clark, X. Y. Lu, A. Kislyuk, Q. Dai, S. W. Turner, C. He, J. Korlach, Nat. Methods 2012, 9, 75. DOI: 10.1038/nmeth.1779
22) C. X. Song, Y. Sun, Q. Dai, X. Y. Lu, M. Yu, C. G. Yang, C. He, ChemBioChem 2011, 12, 1682. DOI: 10.1002/cbic.201100278
23) Z. Liutkeviciute, E. Kriukiene, I. Grigaityte, V. Masevicius, S. Klimasauskas, Angew. Chem. 2011, 123, 2138. DOI: 10.1002/ange.201007169
24) A. S. Hansen, A. Thalhammer, A. H. El-Sagheer, T. Brown, C. J. Schofield, Bioorg. Med. Chem. Lett. 2011, 21, 1181. DOI: 10.1016/j.bmcl.2010.12.098
25) K. Sugizaki, S. Ikeda, H. Yanagisawa, A. Okamoto, Org. Biomol. Chem. 2011, 9, 4176. DOI: 10.1039/c1ob05247k
26) M. Münzel, D. Globisch, C. Trindler, T. Carell, Org. Lett. 2010, 12, 5671. DOI: 10.1021/ol102408t
27) Q. Dai, C. X. Song, T. Pan, C. He, J. Org. Chem. 2011, 76, 4182. DOI: 10.1021/jo200566d
28) M. Münzel, U. Lischke, D. Stathis, T. Pfaffeneder, F. A. Gnerlich, C. A. Deiml, S. C. Koch, K. Karaghiosoff, T. Carell, Chem. Eur. J. 2011, 17, 13782–13788. DOI: 10.1002/chem.201102782
29) Q. Dai, C. He, Org. Lett. 2011, 13, 3446. DOI: 10.1021/ol201189n
30) A. Thalhammer, A. S. Hansen, A. H. El-Sagheer, T. Brown, C. J. Schofield, Chem. Commun. 2011, 47, 5325. DOI: 10.1039/c0cc05671e Recommended summaries on the topic can be found in these review articles: a) M. Münzel, D. Globisch, T. Carell, Angew. Chem. 2011, 123, 6588. DOI: 10.1002/ange.201101547; b) T. P . Jurkowski, A. Jeltsch, ChemBioChem 2011, 12, 2543. DOI: 10.1002/cbic.201100549; c) C. Höbartner, Angew. Chem. 2011, 123, 4357. DOI: 10.1002/ange.201100350; d) M. R. Branco, G. Ficz, W. Reik, Nat. Rev. Genet. 2012, 13, 7. DOI: 10.1038/nrg3080; e) K. I. Ladwein, M. Jung, Angew. Chem. 2011, 123, 12347. DOI: 10.1002/ange.201106690

_{Image: © Wiley-VCH, from ChemBioChem 13/2011 cover}