Nature Genetics Contents: January 2015 pp 1- 97

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TABLE OF CONTENTS January 2015 Volume 47, Issue 1 Editorial News and Views Research Highlights Perspective Articles Letters Corrigenda Subscribe   Facebook   RSS   Recommend to library   Twitter   Editorial Top Modeling transcriptional regulation   p1 doi:10.1038/ng.3188 Systems models of the ways transcription factor networks operate and evolve are essential for understanding cell identity, developmental commitment and regulatory variation. Terminologies from different techniques and disciplines may need to be adapted or put aside to make and test these models effectively. News and Views Top Pseudomonas aeruginosa adaptation to human hosts   pp2 - 3 Evan S Snitkin & Julia A Segre doi:10.1038/ng.3172 Bacterial whole-genome sequencing of longitudinally collected isolates enables the investigation of evolutionary trajectories, which may inform both the prevention and treatment of human-associated pathogen infections. A new study explores the adaptation of multiple lineages of Pseudomonas aeruginosa to the lungs of young patients with cystic fibrosis and finds evidence of convergent molecular evolution and historical contingencies. See also: Article by Marvig et al. A genome to unveil the mysteries of orchids   pp3 - 4 Victor A Albert & Lorenzo Carretero-Paulet doi:10.1038/ng.3179 Orchids have captured imaginations worldwide for hundreds of years. The publication of the moth orchid genome sequence opens the door to a greater understanding of orchid morphological evolution and physiological adaptation. See also: Article by Cai et al. Swapping one red pigment for another   pp5 - 6 Kevin M Davies doi:10.1038/ng.3174 Betalains are bright red and yellow pigments, which are produced in only one order of plants, the Caryophyllales, and replace the more familiar anthocyanin pigments. The evolutionary origin of betalain production is a mystery, but a new study has identified the first regulator of betalain production and discovered a previously unknown link between the two pigment pathways. See also: Letter by Hatlestad et al. Genetics JOBS of the week Postdoctoral Fellow: Statistical Genetics, Computational Biology University of Calfornia, San Diego Postdoctoral Scientist - Genetics Texas Biomedical Research Institute The C. Reed Funk Chair in Plant Genetics and Genomics Rutgers University - New Brunswick Assistant or Associate Professor, Pediatric Diabetes and Metabolic Disease University of California San Diego Health System postdoc University of Michigan Ann Arbor More Science jobs from Genetics EVENT CoGEN: Controversies in preconception, preimplantation and prenatal genetic diagnosis: How will genetics technology drive the future? 25.09.15 Paris, France More science events from Research Highlights Top Replication timing-associated variants | Anopheline mosquito genomes | Regulation of bitterness in cucumber | Clonal evolution of B-ALL | Noncoding mutation in T-ALL Perspective Top What are super-enhancers?   pp8 - 12 Sebastian Pott and Jason D Lieb doi:10.1038/ng.3167 Jason Lieb and Sebastian Pott review the identification and composition of super-enhancers and ask whether super-enhancers are a new, conceptually distinct regulatory entity. Articles Top Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes   pp13 - 21 Steffen Durinck, Eric W Stawiski, Andrea Pavía-Jiménez, Zora Modrusan, Payal Kapur, Bijay S Jaiswal, Na Zhang, Vanina Toffessi-Tcheuyap, Thong T Nguyen, Kanika Bajaj Pahuja, Ying-Jiun Chen, Sadia Saleem, Subhra Chaudhuri, Sherry Heldens, Marlena Jackson, Samuel Peña-Llopis, Joseph Guillory, Karen Toy, Connie Ha, Corissa J Harris, Eboni Holloman, Haley M Hill, Jeremy Stinson, Celina Sanchez Rivers, Vasantharajan Janakiraman, Weiru Wang, Lisa N Kinch, Nick V Grishin, Peter M Haverty, Bernard Chow, Julian S Gehring, Jens Reeder, Gregoire Pau, Thomas D Wu, Vitaly Margulis, Yair Lotan, Arthur Sagalowsky, Ivan Pedrosa, Frederic J de Sauvage, James Brugarolas & Somasekar Seshagiri doi:10.1038/ng.3146 Somasekar Seshagiri, James Brugarolas and colleagues report the mutational landscape of 167 non-clear cell renal cell carcinomas (nccRCCs) from multiple subtypes. They identify subtype-specific driver mutations and gene fusions, including ones involving MITF, which result in expression of the anti-apoptotic protein BIRC7 and might thus indicate candidates for treatment with BIRC7 inhibitors. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence   pp22 - 30 Lei Gu, Sandra C Frommel, Christopher C Oakes, Ronald Simon, Katharina Grupp, Cristina Y Gerig, Dominik Bär, Mark D Robinson, Constance Baer, Melanie Weiss, Zuguang Gu, Matthieu Schapira, Ruprecht Kuner, Holger Sültmann, Maurizio Provenzano, ICGC Project on Early Onset Prostate Cancer, Marie-Laure Yaspo, Benedikt Brors, Jan Korbel, Thorsten Schlomm, Guido Sauter, Roland Eils, Christoph Plass & Raffaella Santoro doi:10.1038/ng.3165 Guido Sauter, Roland Eils, Christoph Plass, Raffaella Santoro and colleagues report that the gene encoding the epigenetic regulator BAZ2A is overexpressed in prostate cancer, where it interacts with EZH2 to induce aberrant gene silencing and cell proliferation. The authors find that BAZ2A levels are predictive of disease recurrence in patients with prostate cancer. Mutations in the deubiquitinase gene USP8 cause Cushing's disease   pp31 - 38 Martin Reincke, Silviu Sbiera, Akira Hayakawa, Marily Theodoropoulou, Andrea Osswald, Felix Beuschlein, Thomas Meitinger, Emi Mizuno-Yamasaki, Kohei Kawaguchi, Yasushi Saeki, Keiji Tanaka, Thomas Wieland, Elisabeth Graf, Wolfgang Saeger, Cristina L Ronchi, Bruno Allolio, Michael Buchfelder, Tim M Strom, Martin Fassnacht & Masayuki Komada doi:10.1038/ng.3166 Martin Reincke, Martin Fassnacht and colleagues identify somatic mutations in the USP8 deubiquitinase gene in corticotroph adenomas in Cushing's disease. The mutations enhanced proteolytic cleavage and catalytic activity of USP8, which led to activation of EGF receptor signaling. A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy   pp39 - 46 Mikko Muona, Samuel F Berkovic, Leanne M Dibbens, Karen L Oliver, Snezana Maljevic, Marta A Bayly, Tarja Joensuu, Laura Canafoglia, Silvana Franceschetti, Roberto Michelucci, Salla Markkinen, Sarah E Heron, Michael S Hildebrand, Eva Andermann, Frederick Andermann, Antonio Gambardella, Paolo Tinuper, Laura Licchetta, Ingrid E Scheffer, Chiara Criscuolo, Alessandro Filla, Edoardo Ferlazzo, Jamil Ahmad, Adeel Ahmad, Betul Baykan, Edith Said, Meral Topcu, Patrizia Riguzzi, Mary D King, Cigdem Ozkara, Danielle M Andrade, Bernt A Engelsen, Arielle Crespel, Matthias Lindenau, Ebba Lohmann, Veronica Saletti, João Massano, Michael Privitera, Alberto J Espay, Birgit Kauffmann, Michael Duchowny, Rikke S Møller, Rachel Straussberg, Zaid Afawi, Bruria Ben-Zeev, Kaitlin E Samocha, Mark J Daly, Steven Petrou, Holger Lerche, Aarno Palotie & Anna-Elina Lehesjoki doi:10.1038/ng.3144 Anna-Elina Lehesjoki and colleagues report exome sequencing of 84 cases of progressive myoclonus epilepsy (PME) and targeted resequencing of an additional 28 cases. They identify de novo mutations in KCNC1 in 13 cases and mutations in genes not previously associated with PME, including PRNP, SACS and TBC1D24, in additional cases. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer   pp47 - 56 Roland Rad, Lena Rad, Wei Wang, Alexander Strong, Hannes Ponstingl, Iraad F Bronner, Matthew Mayho, Katja Steiger, Julia Weber, Maren Hieber, Christian Veltkamp, Stefan Eser, Ulf Geumann, Rupert Öllinger, Magdalena Zukowska, Maxim Barenboim, Roman Maresch, Juan Cadiñanos, Mathias Friedrich, Ignacio Varela, Fernando Constantino-Casas, Aaron Sarver, Jelle ten Hoeve, Haydn Prosser, Barbara Seidler, Judith Bauer, Mathias Heikenwälder, Emmanouil Metzakopian, Anne Krug, Ursula Ehmer, Günter Schneider, Thomas Knösel, Petra Rümmele, Daniela Aust, Robert Grützmann, Christian Pilarsky, Zemin Ning, Lodewyk Wessels, Roland M Schmid, Michael A Quail, George Vassiliou, Irene Esposito, Pentao Liu, Dieter Saur & Allan Bradley doi:10.1038/ng.3164 Roland Rad and colleagues report development of a new conditional piggyBac transposition system for performing insertional mutagenesis screens in mice. They apply the system to identify new oncogenic driver pathways for pancreatic cancer. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis    pp57 - 64 Rasmus Lykke Marvig, Lea Mette Sommer, Søren Molin & Helle Krogh Johansen doi:10.1038/ng.3148 Rasmus Marvig and colleagues report the whole-genome sequencing of 474 longitudinally collected clinical isolates of Pseudomonas aeruginosa sampled from 34 children and young patients with cystic fibrosis. They identify evidence of convergent evolution in 52 genes and suggest pathways involved in within-host adaptation and pathogenesis. See also: News and Views by Snitkin & Segre The genome sequence of the orchid Phalaenopsis equestris OPEN   pp65 - 72 Jing Cai, Xin Liu, Kevin Vanneste, Sebastian Proost, Wen-Chieh Tsai, Ke-Wei Liu, Li-Jun Chen, Ying He, Qing Xu, Chao Bian, Zhijun Zheng, Fengming Sun, Weiqing Liu, Yu-Yun Hsiao, Zhao-Jun Pan, Chia-Chi Hsu, Ya-Ping Yang, Yi-Chin Hsu, Yu-Chen Chuang, Anne Dievart, Jean-Francois Dufayard, Xun Xu, Jun-Yi Wang, Jun Wang, Xin-Ju Xiao, Xue-Min Zhao, Rong Du, Guo-Qiang Zhang, Meina Wang, Yong-Yu Su, Gao-Chang Xie, Guo-Hui Liu, Li-Qiang Li, Lai-Qiang Huang, Yi-Bo Luo, Hong-Hwa Chen, Yves Van de Peer & Zhong-Jian Liu doi:10.1038/ng.3149 Zhong-Jian Liu, Lai-Qiang Huang, Yi-Bo Luo, Hong-Hwa Chen and Yves Van de Peer report the first genome sequence of a crassulacean acid metabolism (CAM) plant, the orchid Phalaenopsis equestris. They identify genes encoding CAM pathway enzymes and find that gene duplication was likely a key process in the evolution of CAM photosynthesis. See also: News and Views by Albert & Carretero-Paulet Letters Top Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy   pp73 - 77 Cas Simons, Lachlan D Rash, Joanna Crawford, Linlin Ma, Ben Cristofori-Armstrong, David Miller, Kelin Ru, Gregory J Baillie, Yasemin Alanay, Adeline Jacquinet, François-Guillaume Debray, Alain Verloes, Joseph Shen, Gözde Yesil, Serhat Guler, Adnan Yuksel, John G Cleary, Sean M Grimmond, Julie McGaughran, Glenn F King, Michael T Gabbett & Ryan J Taft doi:10.1038/ng.3153 Cas Simons, Ryan Taft and colleagues report the identification of KCNH1 mutations in six individuals with Temple-Baraitser syndrome (TBS). Electrophysiological measurements of cells expressing mutant KCNH1 channels show decreased activation thresholds and slower deactivation in comparison to wild-type channels, suggesting that these mutations lead to gain of function of KCNH1. Common variation in PHACTR1 is associated with susceptibility to cervical artery dissection   pp78 - 83 Stéphanie Debette, Yoichiro Kamatani, Tiina M Metso, Manja Kloss, Ganesh Chauhan, Stefan T Engelter, Alessandro Pezzini, Vincent Thijs, Hugh S Markus, Martin Dichgans, Christiane Wolf, Ralf Dittrich, Emmanuel Touzé, Andrew M Southerland, Yves Samson, Shérine Abboud, Yannick Béjot, Valeria Caso, Anna Bersano, Andreas Gschwendtner, Maria Sessa, John Cole, Chantal Lamy, Elisabeth Medeiros, Simone Beretta, Leo H Bonati, Armin J Grau, Patrik Michel, Jennifer J Majersik, Pankaj Sharma, Ludmila Kalashnikova, Maria Nazarova, Larisa Dobrynina, Eva Bartels, Benoit Guillon, Evita G van den Herik, Israel Fernandez-Cadenas, Katarina Jood, Michael A Nalls, Frank-Erik De Leeuw, Christina Jern, Yu-Ching Cheng, Inge Werner, Antti J Metso, Christoph Lichy, Philippe A Lyrer, Tobias Brandt, Giorgio B Boncoraglio, Heinz-Erich Wichmann, Christian Gieger, Andrew D Johnson, Thomas Böttcher, Maurizio Castellano, Dominique Arveiler, M Arfan Ikram, Monique M B Breteler, Alessandro Padovani, James F Meschia, Gregor Kuhlenbäumer, Arndt Rolfs, Bradford B Worrall, International Stroke Genetics Consortium, Erich-Bernd Ringelstein, Diana Zelenika, Turgut Tatlisumak, Mark Lathrop, Didier Leys, the CADISP group, Philippe Amouyel & Jean Dallongeville doi:10.1038/ng.3154 Stéphanie Debette and colleagues report the results of a genome-wide association study of cervical artery dissection, a major cause of ischemic stroke in young adults. They show that common variation in PHACTR1, previously associated with lower risk of migraine and increased risk of myocardial infarction, is associated with reduced risk of cervical artery dissection. Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance   pp84 - 87 Mark R Davies, Matthew T Holden, Paul Coupland, Jonathan H K Chen, Carola Venturini, Timothy C Barnett, Nouri L Ben Zakour, Herman Tse, Gordon Dougan, Kwok-Yung Yuen & Mark J Walker doi:10.1038/ng.3147 Mark Walker and colleagues report the whole-genome sequencing of 132 group A Streptococcus (GAS) isolates of a sequence type that has been associated with scarlet fever. The isolates were obtained from 58 clinical cases of scarlet fever and 83 cases without scarlet fever during the course of a recent epidemic in Hong Kong. Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins   pp88 - 91 Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector & Emmanouil T Dermitzakis doi:10.1038/ng.3162 Emmanouil Dermitzakis, Alfonso Buil and colleagues measure transcriptome-wide expression in a sample of twins to measure the relative contribution of genetic and environmental effects on allele-specific expression and find substantial effects of gene [times] gene and gene [times] environment interactions. The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pathway   pp92 - 96 Gregory J Hatlestad, Neda A Akhavan, Rasika M Sunnadeniya, Lee Elam, Scott Cargile, Austin Hembd, Antonio Gonzalez, J Mitchell McGrath & Alan M Lloyd doi:10.1038/ng.3163 Alan Lloyd and colleagues identify a MYB gene in beet that acts as a key regulator of the betalain red pigmentation pathway. They further show that this gene resides at the classical Y pigmentation locus and shares homology with MYB genes that encode positive regulators of the anthocyanin pigmentation pathway in other species. See also: News and Views by Davies Corrigenda Top Corrigendum: SPRTN is a new player in an old story   p97 Kevin Hiom doi:10.1038/ng0115-97a Corrigendum: Identification of recurrent SMO and BRAF mutations in ameloblastomas   p97 Robert T Sweeney, Andrew C McClary, Benjamin R Myers, Jewison Biscocho, Lila Neahring, Kevin A Kwei, Kunbin Qu, Xue Gong, Tony Ng, Carol D Jones, Sushama Varma, Justin I Odegaard, Toshihiro Sugiyama, Souichi Koyota, Brian P Rubin, Megan L Troxell, Robert J Pelham, James L Zehnder, Philip A Beachy, Jonathan R Pollack & Robert B West doi:10.1038/ng0115-97b Top Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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