Nature Genetics Contents: February 2012 pp 111 - 232

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Subscribe   Facebook   RSS   Recommend to library   Twitter   Announcing the Cell Symposia on Genetics and Chemistry Sharing a Language of Discovery - May 23-25, 2012 - Boston Marriott Cambridge, Cambridge, MA, USA. Submit your abstract here before February 17, 2012 for consideration in our poster program and register before March 30, 2012 to save $100! We look forward to seeing you all Cambridge, USA!   Advertisement Nature Reprint Collection: microRNAs This collection of recent papers from Nature and other NPG journals highlights developments in microRNA biology and effects on gene regulation. Access the reprint collection free online for six months. Produced with support from: Regulus Therapeutics Inc.   Editorial Top It's not about the data p111 doi:10.1038/ng.1099 Researchers, funders and journals are in broad agreement that data must be accessible to support the conclusions of scientific publications and for the research to have impact. What is lacking is agreement on timing, formatting and attribution. Full Text | PDF Correspondence Top The authorship network of genome-wide association studies p113 Brendan K. Bulik-Sullivan and Patrick F. Sullivan doi:10.1038/ng.1052 Full Text | PDF Book Review Top A digital examination of medicine p114 Hadrian A L Green reviews The Creative Destruction of Medicine: How the Digital Revolution Will Create Better Healthcare by Eric Topol doi:10.1038/ng.1101 Full Text | PDF News and Views Top Arabidopsis thaliana as a model for the genetics of local adaptation pp115 - 116 Brandon Gaut doi:10.1038/ng.1079 A new study reports SNP genotypes of over 1,300 Arabidopsis thaliana accessions from throughout Eurasia, providing a resource for genome-wide association studies and studies of local adaptation. The extensive data are also used to identify targets of natural selection and to describe genome-wide patterns of recombination. Full Text | PDF See also: Letter by Horton et al. The genome of a blood fluke associated with human cancer pp116 - 118 Makedonka Mitreva doi:10.1038/ng.1082 The sequencing of the genome and transcriptome of Schistosoma haematobium, a highly prevalent blood fluke and human parasite with a proven link to malignant bladder cancer, marks the 160th anniversary of its discovery as the first schistosome known to infect humans. Comparative genomic analyses of S. haematobium and the more prevalent human-schistosomiasis pathogens (Schistosoma mansoni and Schistosoma japonicum) identified both shared and distinct genomic features. Full Text | PDF See also: Letter by Young et al. The persistence of a silent memory pp118 - 119 Mikel Zaratiegui and Robert Martienssen doi:10.1038/ng.1088 One of the most striking properties of RNA interference (RNAi) in Caenorhabditis elegans is its persistence in offspring after the triggering double-stranded RNA (dsRNA) has disappeared. A new study reveals that a heterochromatic silencing mark is deposited around the targets of RNAi and is transmitted through generations. These results show that RNAi can induce stable and heritable chromatin modifications in animals. Full Text | PDF See also: Article by Gu et al. Genetics JOBS of the week Network Biology Team Leader Kelly Scientific Resources postdoc fellow Oakland University Wellcome Trust Oxion Training Fellow University of Oxford Research Associate (Asst Prof / Assoc Prof), cancer genetics / genomics Univeristy of Chicago PhD Students in Molecular Medicine Laboratory for Molecular Infection Medicine Sweden (MIMS) / Nordic EMBL Partnership More Science jobs from Genetics EVENT Complex Traits: Genomics and Computational Approaches (B5) 20.-25.02.12 CO, US More science events from Research Highlights Top SIRT1 and anxiety | Gregarious locusts | DICER1 in ovarian cancers | Genomics of endangered primates | Cardiac symptoms of Rett syndrome Commentary Top Toward interoperable bioscience data pp121 - 126 Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler, Kimberly Begley, Tim Booth, Lydie Bougueleret, Gully Burns, Brad Chapman, Tim Clark, Lee-Ann Coleman, Jay Copeland, Sudeshna Das, Antoine de Daruvar, Paula de Matos, Ian Dix, Scott Edmunds, Chris T Evelo, Mark J Forster, Pascale Gaudet, Jack Gilbert, Carole Goble, Julian L Griffin, Daniel Jacob, Jos Kleinjans, Lee Harland, Kenneth Haug, Henning Hermjakob, Shannan J Ho Sui, Alain Laederach, Shaoguang Liang, Stephen Marshall, Annette McGrath, Emily Merrill, Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, Katherine Wolstencroft, Ioannis Xenarios & Winston Hide doi:10.1038/ng.1054 Abstract | Full Text | PDF Perspective Top Developing predictive molecular maps of human disease through community-based modeling pp127 - 130 Jonathan M J Derry, Lara M Mangravite, Christine Suver, Matthew D Furia, David Henderson, Xavier Schildwachter, Brian Bot, Jonathan Izant, Solveig K Sieberts, Michael R Kellen and Stephen H Friend doi:10.1038/ng.1089 Full Text | PDF Brief Communication Top ABCG2 null alleles define the Jr(a-) blood group phenotype pp131 - 132 Teresa Zelinski, Gail Coghlan, Xiao-Qing Liu and Marion E Reid doi:10.1038/ng.1075 Teresa Zelinski and colleagues identify null alleles of ABCG2 in individuals with the Jr(a-) blood group phenotype. First paragraph | Full Text | PDF Articles Top Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma pp133 - 139 Sergey I Nikolaev, Donata Rimoldi, Christian Iseli, Armand Valsesia, Daniel Robyr, Corinne Gehrig, Keith Harshman, Michel Guipponi, Olesya Bukach, Vincent Zoete, Olivier Michielin, Katja Muehlethaler, Daniel Speiser, Jacques S Beckmann, Ioannis Xenarios, Thanos D Halazonetis, C Victor Jongeneel, Brian J Stevenson & Stylianos E Antonarakis doi:10.1038/ng.1026 Sergey Nikolaev, Stylianos Antonarakis and colleagues report exome sequencing of seven melanoma cell lines and matched germline cells. They identify recurring somatic mutations in MAP2K1 and MAP2K2 occurring at an overall frequency of 8%. Abstract | Full Text | PDF PNPLA1 mutations cause autosomal recessive congenital ichthyosis in golden retriever dogs and humans pp140 - 147 Anaïs Grall, Eric Guaguère, Sandrine Planchais, Susanne Grond, Emmanuelle Bourrat, Ingrid Hausser, Christophe Hitte, Matthieu Le Gallo, Céline Derbois, Gwang-Jin Kim, Laëtitia Lagoutte, Frédérique Degorce-Rubiales, Franz P W Radner, Anne Thomas, Sébastien Küry, Emmanuel Bensignor, Jacques Fontaine, Didier Pin, Robert Zimmermann, Rudolf Zechner, Mark Lathrop, Francis Galibert, Catherine André & Judith Fischer doi:10.1038/ng.1056 Catherine André, Judith Fischer and colleagues report that mutations in PNPLA1 cause congenital ichthyosis in humans and golden retriever dogs. Their findings suggest a role for PNPLA1 in the formation of the epidermal lipid barrier. Abstract | Full Text | PDF Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development pp148 - 156 Stefan Bonn, Robert P Zinzen, Charles Girardot, E Hilary Gustafson, Alexis Perez-Gonzalez, Nicolas Delhomme, Yad Ghavi-Helm, Bartek Wilczynski, Andrew Riddell and Eileen E M Furlong doi:10.1038/ng.1064 Eileen Furlong and colleagues report the development and application of BiTS-ChIP (batch isolate tissue specific chromatin immunoprecipitation), in which a tagged nuclear protein is expressed in developing cells of interest. They apply this method to investigate six chromatin markers and RNA Pol II occupancy in mesodermal cells in developing Drosophila embryos and find that histone modifications and Pol II occupancy can predict enhancer activity. Abstract | Full Text | PDF Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint pp157 - 164 Sam Guoping Gu, Julia Pak, Shouhong Guang, Jay M Maniar, Scott Kennedy and Andrew Fire doi:10.1038/ng.1039 Andy Fire and colleagues report the finding of histone H3 lysine 9 trimethylation footprints extending several kilobases from siRNA targets at specific loci across the C. elegans genome. Such exogenous RNA-induced chromatin modification was mediated by secondary amplification of siRNA and was maintained across two or more generations. Abstract | Full Text | PDF See also: News and Views by Zaratiegui & Martienssen Letters Top Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing pp165 - 169 Mitchell S Stark, Susan L Woods, Michael G Gartside, Vanessa F Bonazzi, Ken Dutton-Regester, Lauren G Aoude, Donald Chow, Chris Sereduk, Natalie M Niemi, Nanyun Tang, Jonathan J Ellis, Jeffrey Reid, Victoria Zismann, Sonika Tyagi, Donna Muzny, Irene Newsham, YuanQing Wu, Jane M Palmer, Thomas Pollak, David Youngkin, Bradford R Brooks, Catherine Lanagan, Christopher W Schmidt, Bostjan Kobe, Jeffrey P MacKeigan, Hongwei Yin, Kevin M Brown, Richard Gibbs, Jeffrey Trent & Nicholas K Hayward doi:10.1038/ng.1041 Nicholas Hayward and colleagues sequenced eight metastatic melanoma exomes and identified frequent somatic mutations in two MAP kinase family genes, MAP3K5 and MAP3K9. Mutation in MAP3K9 may confer resistance to temozolomide, a common chemotherapeutic drug. First paragraph | Full Text | PDF ABCB6 is dispensable for erythropoiesis and specifies the new blood group system Langereis pp170 - 173 Virginie Helias, Carole Saison, Bryan A Ballif, Thierry Peyrard, Junko Takahashi, Hideo Takahashi, Mitsunobu Tanaka, Jean-Charles Deybach, Herve Puy, Maude Le Gall, Camille Sureau, Bach-Nga Pham, Pierre-Yves Le Pennec, Yoshihiko Tani, Jean-Pierre Cartron and Lionel Arnaud doi:10.1038/ng.1069 Lionel Arnaud and colleagues identify ABCB6 as the genetic basis of the novel Lan blood group system. First paragraph | Full Text | PDF Null alleles of ABCG2 encoding the breast cancer resistance protein define the new blood group system Junior pp174 - 177 Carole Saison, Virginie Helias, Bryan A Ballif, Thierry Peyrard, Hervé Puy, Toru Miyazaki, Sébastien Perrot, Muriel Vayssier-Taussat, Mauro Waldner, Pierre-Yves Le Pennec, Jean-Pierre Cartron & Lionel Arnaud doi:10.1038/ng.1070 Lionel Arnaud and colleagues identify null alleles of ABCG2 as the genetic basis of the Junior blood group system. First paragraph | Full Text | PDF A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy pp178 - 182 Xue-Qing Yu, Ming Li, Hong Zhang, Hui-Qi Low, Xin Wei, Jin-Quan Wang, Liang-Dan Sun, Kar-Seng Sim, Yi Li, Jia-Nee Foo, Wei Wang, Zhi-Jian Li, Xian-Yong Yin, Xue-Qing Tang, Li Fan, Jian Chen, Rong-Shan Li, Jian-Xin Wan, Zhang-Suo Liu, Tan-Qi Lou, Li Zhu, Xiao-Jun Huang, Xue-Jun Zhang, Zhi-Hong Liu and Jian-Jun Liu doi:10.1038/ng.1047 Xue-Qing Yu, Jian-Jun Liu and colleagues report results of a genome-wide association study of IgA nephropathy in Han Chinese. They identify two new susceptibility loci at 8p23 and 17p13 and replicate previously reported signals in the MHC region and at 22q12. First paragraph | Full Text | PDF A genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia pp183 - 186 Zhibin Hu, Yankai Xia, Xuejiang Guo, Juncheng Dai, HongGang Li, Hongliang Hu, Yue Jiang, Feng Lu, Yibo Wu, Xiaoyu Yang, Huizhang Li, Bing Yao, Chuncheng Lu, Chenliang Xiong, Zheng Li, Yaoting Gui, Jiayin Liu, Zuomin Zhou, Hongbing Shen, Xinru Wang and Jiahao Sha doi:10.1038/ng.1040 Jiahao Sha, Xinru Wang, Hongbing Shen and colleagues report a genome-wide association study of non-obstructive azoospermia in Chinese men. They identify common variants near three genes (PRMT6, PEX10 and SOX5) associated with this form of male infertility. First paragraph | Full Text | PDF Meta-analysis of genome-wide association studies identifies three new risk loci for atopic dermatitis pp187 - 192 Lavinia Paternoster, Marie Standl, Chih-Mei Chen, Adaikalavan Ramasamy, Klaus Bønnelykke, Liesbeth Duijts, Manuel A Ferreira, Alexessander Couto Alves, Jacob P Thyssen, Eva Albrecht, Hansjörg Baurecht, Bjarke Feenstra, Patrick M A Sleiman, Pirro Hysi, Nicole M Warrington, Ivan Curjuric, Ronny Myhre, John A Curtin, Maria M Groen-Blokhuis, Marjan Kerkhof, Annika Sääf, Andre Franke, David Ellinghaus, Regina Fölster-Holst, Emmanouil Dermitzakis, Stephen B Montgomery, Holger Prokisch, Katharina Heim, Anna-Liisa Hartikainen, Anneli Pouta, Juha Pekkanen, Alexandra I F Blakemore, Jessica L Buxton, Marika Kaakinen, David L Duffy, Pamela A Madden, Andrew C Heath, Grant W Montgomery, Philip J Thompson, Melanie C Matheson, Peter Le Souëf, Australian Asthma Genetics Consortium (AAGC), Beate St. Pourcain, George Davey Smith, John Henderson, John P Kemp, Nicholas J Timpson, Panos Deloukas, Susan M Ring, H-Erich Wichmann, Martina Müller-Nurasyid, Natalija Novak, Norman Klopp, Elke Rodríguez, Wendy McArdle, Allan Linneberg, Torkil Menné, Ellen A Nohr, Albert Hofman, André G Uitterlinden, Cornélia M van Duijn, Fernando Rivadeneira, Johan C de Jongste, Ralf J P van der Valk, Matthias Wjst, Rain Jogi, Frank Geller, Heather A Boyd, Jeffrey C Murray, Cecilia Kim, Frank Mentch, Michael March, Massimo Mangino, Tim D Spector, Veronique Bataille, Craig E Pennell, Patrick G Holt, Peter Sly, Carla M T Tiesler, Elisabeth Thiering, Thomas Illig, Medea Imboden, Wenche Nystad, Angela Simpson, Jouke-Jan Hottenga, Dirkje Postma, Gerard H Koppelman, Henriette A Smit, Cilla Söderhäll, Bo Chawes, Eskil Kreiner-Møller, Hans Bisgaard, Erik Melén, Dorret I Boomsma, Adnan Custovic, Bo Jacobsson, Nicole M Probst-Hensch, Lyle J Palmer, Daniel Glass, Hakon Hakonarson, Mads Melbye, Deborah L Jarvis, Vincent W V Jaddoe, Christian Gieger, The Genetics of Overweight Young Adults (GOYA) Consortium, David P Strachan, Nicholas G Martin, Marjo-Riitta Jarvelin, Joachim Heinrich, David M Evans & Stephan Weidinger for the EArly Genetics & Lifecourse Epidemiology (EAGLE) Consortium doi:10.1038/ng.1017 Lavinia Paternoster and colleagues report a meta-analysis of genome-wide association studies of atopic dermatitis. They report three newly identified associated loci near OVOL1 and ACTL9 and in KIF3A. First paragraph | Full Text | PDF CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium pp193 - 199 Ji Eun Lee, Jennifer L Silhavy, Maha S Zaki, Jana Schroth, Stephanie L Bielas, Sarah E Marsh, Jesus Olvera, Francesco Brancati, Miriam Iannicelli, Koji Ikegami, Andrew M Schlossman, Barry Merriman, Tania Attié-Bitach, Clare V Logan, Ian A Glass, Andrew Cluckey, Carrie M Louie, Jeong Ho Lee, Hilary R Raynes, Isabelle Rapin, Ignacio P Castroviejo, Mitsutoshi Setou, Clara Barbot, Eugen Boltshauser, Stanley F Nelson, Friedhelm Hildebrandt, Colin A Johnson, Daniel A Doherty, Enza Maria Valente & Joseph G Gleeson doi:10.1038/ng.1078 Joseph Gleeson and colleagues identify CEP41 mutations as a cause of Joubert syndrome. Their functional studies suggest that CEP41 regulates ciliary entry of TTLL6, an enzyme required for tubulin glutamylation at the cilium. First paragraph | Full Text | PDF Mutations in the colony stimulating factor 1 receptor (CSF1R) gene cause hereditary diffuse leukoencephalopathy with spheroids pp200 - 205 Rosa Rademakers, Matt Baker, Alexandra M Nicholson, Nicola J Rutherford, NiCole Finch, Alexandra Soto-Ortolaza, Jennifer Lash, Christian Wider, Aleksandra Wojtas, Mariely DeJesus-Hernandez, Jennifer Adamson, Naomi Kouri, Christina Sundal, Elizabeth A Shuster, Jan Aasly, James MacKenzie, Sigrun Roeber, Hans A Kretzschmar, Bradley F Boeve, David S Knopman, Ronald C Petersen, Nigel J Cairns, Bernardino Ghetti, Salvatore Spina, James Garbern, Alexandros C Tselis, Ryan Uitti, Pritam Das, Jay A Van Gerpen, James F Meschia, Shawn Levy, Daniel F Broderick, Neill Graff-Radford, Owen A Ross, Bradley B Miller, Russell H Swerdlow, Dennis W Dickson & Zbigniew K Wszolek doi:10.1038/ng.1027 Rosa Rademakers and colleagues show that mutations in CSF1R cause hereditary diffuse leukoencephalopathy with spheroids, a central nervous system white-matter disease with variable clinical presentations that include personality and behavioral changes, dementia, depression, parkinsonism and seizures. First paragraph | Full Text | PDF Crh and Oprm1 mediate anxiety-related behavior and social approach in a mouse model of MECP2 duplication syndrome pp206 - 211 Rodney C Samaco, Caleigh Mandel-Brehm, Christopher M McGraw, Chad A Shaw, Bryan E McGill and Huda Y Zoghbi doi:10.1038/ng.1066 Huda Zoghbi and colleagues report that MECP2 transgenic mice display heightened anxiety and social approach deficits and that genetic and pharmacological inhibition of Crh or its receptor, Crhr1, suppresses the anxiety phenotypes. The authors also report that genetic reduction of Oprm1 improves social approach behaviors in MECP2 transgenic mice. First paragraph | Full Text | PDF Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel pp212 - 216 Matthew W Horton, Angela M Hancock, Yu S Huang, Christopher Toomajian, Susanna Atwell, Adam Auton, N Wayan Muliyati, Alexander Platt, F Gianluca Sperone, Bjarni J Vilhjálmsson, Magnus Nordborg, Justin O Borevitz & Joy Bergelson doi:10.1038/ng.1042 Joy Bergelson and colleagues characterize genome-wide patterns of genetic variation in a collection of 1,307 worldwide Arabidopsis thaliana accessions from the Regional Mapping (RegMap) panel, a publicly available genomic resource that includes large regional panels. They characterize signatures of selection and patterns of recombination and identify an enrichment of hotspots in intergenic regions and in repetitive DNA. First paragraph | Full Text | PDF See also: News and Views by Gaut Genomic and metabolic prediction of complex heterotic traits in hybrid maize pp217 - 220 Christian Riedelsheimer, Angelika Czedik-Eysenberg, Christoph Grieder, Jan Lisec, Frank Technow, Ronan Sulpice, Thomas Altmann, Mark Stitt, Lothar Willmitzer and Albrecht E Melchinger doi:10.1038/ng.1033 Albrecht Melchinger and colleagues report a complementary approach to phenotype-based screening for hybrid maize. The new approach accurately predicts the combining abilities of agronomical traits based on genomic and metabolomic information comprising 56,110 SNPs and 130 metabolite measurements. First paragraph | Full Text | PDF Whole-genome sequence of Schistosoma haematobium  pp221 - 225 Neil D Young, Aaron R Jex, Bo Li, Shiping Liu, Linfeng Yang, Zijun Xiong, Yingrui Li, Cinzia Cantacessi, Ross S Hall, Xun Xu, Fangyuan Chen, Xuan Wu, Adhemar Zerlotini, Guilherme Oliveira, Andreas Hofmann, Guojie Zhang, Xiaodong Fang, Yi Kang, Bronwyn E Campbell, Alex Loukas, Shoba Ranganathan, David Rollinson, Gabriel Rinaldi, Paul J Brindley, Huanming Yang, Jun Wang, Jian Wang and Robin B Gasser doi:10.1038/ng.1065 Robin Gasser and his colleagues report the whole-genome sequence of Schistosoma haematobium. They include comparisons to the genome sequences of S. mansoni and S. japonicum, the two other species that cause schistosomiasis in humans. First paragraph | Full Text | PDF See also: News and Views by Mitreva Technical Report Top De novo assembly and genotyping of variants using colored de Bruijn graphs pp226 - 232 Zamin Iqbal, Mario Caccamo, Isaac Turner, Paul Flicek and Gil McVean doi:10.1038/ng.1028 Gil McVean and colleagues report algorithms for de novo assembly and genotyping of variants using colored de Bruijn graphs and provide these in a software implementation called Cortex. Their methods can detect and genotype both simple and complex genetic variants in either an individual or a population. Abstract | Full Text | PDF Top Advertisement Nature Reviews Genetics ANIMATION ON RNA INTERFERENCE Nature Reviews Genetics, in association with Arkitek Studios, has brought RNAi to life in this vivid, audio-visual journey into the cell. 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