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Table of Contents: September 2012

COVER

Diversity in lung metastasis.

Image Credit: Farhoud Faraji and Thomas Geiger.
Issue Image

The lungs are the most common site of breast cancer metastasis. Metastatic efficiency is dictated by a complex interplay of tumor-intrinsic and host-derived factors. Allelic variability in the germline can be a major determinant of these factors, signifying that a heritable component contributes to an individual's propensity to develop metastatic disease. In this issue, Faraji et al. identify Cadm1 expression as a heritable metastasis susceptibility factor and show that tumor-intrinsic Cadm1 expression interacts with tumor-extrinsic T-cell–mediated immunity to modulate the efficiency of tumor cell metastasis to the lungs.

Perspectives

The Long Path from QTL to Gene

Norman R. Drinkwater, Michael N. Gould

Research Articles

Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles

Ella R. Thompson, Maria A. Doyle, Georgina L. Ryland, Simone M. Rowley, David Y. H. Choong, Richard W. Tothill, Heather Thorne, Daniel R. Barnes, Jason Li, Jason Ellul, Gayle K. Philip, Yoland C. Antill, Paul A. James, Alison H. Trainer, Gillian Mitchell, Ian G. Campbell , kConFab

Role of Transposon-Derived Small RNAs in the Interplay between Genomes and Parasitic DNA in Rice

Misuzu Nosaka, Jun-Ichi Itoh, Yasuo Nagato, Akemi Ono, Aiko Ishiwata, Yutaka Sato

Determinants of Human Adipose Tissue Gene Expression: Impact of Diet, Sex, Metabolic Status, and Cis Genetic Regulation

Nathalie Viguerie, Emilie Montastier, Jean-José Maoret, Balbine Roussel, Marion Combes, Carine Valle, Nathalie Villa-Vialaneix, Jason S. Iacovoni, J. Alfredo Martinez, Claus Holst, Arne Astrup, Hubert Vidal, Karine Clément, Jorg Hager, Wim H. M. Saris, Dominique Langin

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals

Frank W. Albert, Mehmet Somel, Miguel Carneiro, Ayinuer Aximu-Petri, Michel Halbwax, Olaf Thalmann, Jose A. Blanco-Aguiar, Irina Z. Plyusnina, Lyudmila Trut, Rafael Villafuerte, Nuno Ferrand, Sylvia Kaiser, Per Jensen, Svante Pääbo

UTX and UTY Demonstrate Histone Demethylase-Independent Function in Mouse Embryonic Development

Karl B. Shpargel, Toru Sengoku, Shigeyuki Yokoyama, Terry Magnuson

SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae

Mickaël Durand-Dubief, William Ryan Will, Edoardo Petrini, Delphine Theodorou, Rachael R. Harris, Margaret R. Crawford, Konrad Paszkiewicz, Felix Krueger, Rosa Maria Correra, Anna T. Vetter, J. Ross Miller, Nicholas A. Kent, Patrick Varga-Weisz

The p38/MK2-Driven Exchange between Tristetraprolin and HuR Regulates AU–Rich Element–Dependent Translation

Christopher Tiedje, Natalia Ronkina, Mohammad Tehrani, Sonam Dhamija, Kathrin Laass, Helmut Holtmann, Alexey Kotlyarov, Matthias Gaestel

Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding

Falk Butter, Lucy Davison, Tar Viturawong, Marion Scheibe, Michiel Vermeulen, John A. Todd, Matthias Mann

TCF7L2 Modulates Glucose Homeostasis by Regulating CREB- and FoxO1-Dependent Transcriptional Pathway in the Liver

Kyoung-Jin Oh, Jinyoung Park, Su Sung Kim, Hyunhee Oh, Cheol Soo Choi, Seung-Hoi Koo

A Mimicking-of-DNA-Methylation-Patterns Pipeline for Overcoming the Restriction Barrier of Bacteria

Guoqiang Zhang, Wenzhao Wang, Aihua Deng, Zhaopeng Sun, Yun Zhang, Yong Liang, Yongsheng Che, Tingyi Wen

New Susceptibility Loci Associated with Kidney Disease in Type 1 Diabetes

Niina Sandholm, Rany M. Salem, Amy Jayne McKnight, Eoin P. Brennan, Carol Forsblom, Tamara Isakova, Gareth J. McKay, Winfred W. Williams, Denise M. Sadlier, Ville-Petteri Mäkinen, Elizabeth J. Swan, Cameron Palmer, Andrew P. Boright, Emma Ahlqvist, Harshal A. Deshmukh, Benjamin J. Keller, Huateng Huang, Aila J. Ahola, Emma Fagerholm, Daniel Gordin, Valma Harjutsalo, Bing He, Outi Heikkilä, Kustaa Hietala, Janne Kytö, Päivi Lahermo, Markku Lehto, Raija Lithovius, Anne-May Österholm, Maija Parkkonen, Janne Pitkäniemi, Milla Rosengård-Bärlund, Markku Saraheimo, Cinzia Sarti, Jenny Söderlund, Aino Soro-Paavonen, Anna Syreeni, Lena M. Thorn, Heikki Tikkanen, Nina Tolonen, Karl Tryggvason, Jaakko Tuomilehto, Johan Wadén, Geoffrey V. Gill, Sarah Prior, Candace Guiducci, Daniel B. Mirel, Andrew Taylor, S. Mohsen Hosseini, Hans-Henrik Parving, Peter Rossing, Lise Tarnow, Claes Ladenvall, François Alhenc-Gelas, Pierre Lefebvre, Vincent Rigalleau, Ronan Roussel, David-Alexandre Tregouet, Anna Maestroni, Silvia Maestroni, Henrik Falhammar, Tianwei Gu, Anna Möllsten, Danut Cimponeriu, Mihai Ioana, Maria Mota, Eugen Mota, Cristian Serafinceanu, Monica Stavarachi, Robert L. Hanson, Robert G. Nelson, Matthias Kretzler, Helen M. Colhoun, Nicolae Mircea Panduru, Harvest F. Gu, Kerstin Brismar, Gianpaolo Zerbini, Samy Hadjadj, Michel Marre, Leif Groop, Maria Lajer, Shelley B. Bull, Daryl Waggott, Andrew D. Paterson, David A. Savage, Stephen C. Bain, Finian Martin, Joel N. Hirschhorn, Catherine Godson, Jose C. Florez, Per-Henrik Groop, Alexander P. Maxwell , DCCT/EDIC Research Group

Cadm1 Is a Metastasis Susceptibility Gene That Suppresses Metastasis by Modifying Tumor Interaction with the Cell-Mediated Immunity

Farhoud Faraji, Yanli Pang, Renard C. Walker, Rosan Nieves Borges, Li Yang, Kent W. Hunter

An Essential Role of Variant Histone H3.3 for Ectomesenchyme Potential of the Cranial Neural Crest

Samuel G. Cox, Hyunjung Kim, Aaron Timothy Garnett, Daniel Meulemans Medeiros, Woojin An, J. Gage Crump

Characterization of Inducible Models of Tay-Sachs and Related Disease

Timothy J. Sargeant, Deborah J. Drage, Susan Wang, Apostolos A. Apostolakis, Timothy M. Cox, M. Begoña Cachón-González

Co-Evolution of Mitochondrial tRNA Import and Codon Usage Determines Translational Efficiency in the Green Alga Chlamydomonas

Thalia Salinas, Francéline Duby, Véronique Larosa, Nadine Coosemans, Nathalie Bonnefoy, Patrick Motte, Laurence Maréchal-Drouard, Claire Remacle

The NDR Kinase Scaffold HYM1/MO25 Is Essential for MAK2 MAP Kinase Signaling in Neurospora crassa

Anne Dettmann, Julia Illgen, Sabine März, Timo Schürg, Andre Fleissner, Stephan Seiler

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

Thanasis Margaritis, Vincent Oreal, Nathalie Brabers, Laetitia Maestroni, Adeline Vitaliano-Prunier, Joris J. Benschop, Sander van Hooff, Dik van Leenen, Catherine Dargemont, Vincent Géli, Frank C. P. Holstege

Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain

Nicole C. Riddle, Youngsook L. Jung, Tingting Gu, Artyom A. Alekseyenko, Dalal Asker, Hongxing Gui, Peter V. Kharchenko, Aki Minoda, Annette Plachetka, Yuri B. Schwartz, Michael Y. Tolstorukov, Mitzi I. Kuroda, Vincenzo Pirrotta, Gary H. Karpen, Peter J. Park, Sarah C. R. Elgin

Tetraspanin Is Required for Generation of Reactive Oxygen Species by the Dual Oxidase System in Caenorhabditis elegans

Hiroki Moribe, Ryouji Konakawa, Daisuke Koga, Tatsuo Ushiki, Kuniaki Nakamura, Eisuke Mekada

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms

Anne-Laure Abraham, Muniyandi Nagarajan, Jean-Baptiste Veyrieras, Hélène Bottin, Lars M. Steinmetz, Gaël Yvert

Rif2 Promotes a Telomere Fold-Back Structure through Rpd3L Recruitment in Budding Yeast

Heiko Poschke, Martina Dees, Michael Chang, Sandeep Amberkar, Lars Kaderali, Rodney Rothstein, Brian Luke

De Novo CNV Formation in Mouse Embryonic Stem Cells Occurs in the Absence of Xrcc4-Dependent Nonhomologous End Joining

Martin F. Arlt, Sountharia Rajendran, Shanda R. Birkeland, Thomas E. Wilson, Thomas W. Glover

Factors That Promote H3 Chromatin Integrity during Transcription Prevent Promiscuous Deposition of CENP-ACnp1 in Fission Yeast

Eun Shik Choi, Annelie Strålfors, Sandra Catania, Araceli G. Castillo, J. Peter Svensson, Alison L. Pidoux, Karl Ekwall, Robin C. Allshire

Variation in Genes Related to Cochlear Biology Is Strongly Associated with Adult-Onset Deafness in Border Collies

Jennifer S. Yokoyama, Ernest T. Lam, Alison L. Ruhe, Carolyn A. Erdman, Kathryn R. Robertson, Aubrey A. Webb, D. Colette Williams, Melanie L. Chang, Marjo K. Hytönen, Hannes Lohi, Steven P. Hamilton, Mark W. Neff

A Genetic Basis for a Postmeiotic X Versus Y Chromosome Intragenomic Conflict in the Mouse

Julie Cocquet, Peter J. I. Ellis, Shantha K. Mahadevaiah, Nabeel A. Affara, Daniel Vaiman, Paul S. Burgoyne

Genome-Wide Association Study for Serum Complement C3 and C4 Levels in Healthy Chinese Subjects

Xiaobo Yang, Jielin Sun, Yong Gao, Aihua Tan, Haiying Zhang, Yanling Hu, Junjie Feng, Xue Qin, Sha Tao, Zhuo Chen, Seong-Tae Kim, Tao Peng, Ming Liao, Xiaoling Lin, Zengfeng Zhang, Minzhong Tang, Li Li, Linjian Mo, Zhengjia Liang, Deyi Shi, Zhang Huang, Xianghua Huang, Ming Liu, Qian Liu, Shijun Zhang, Jeffrey M. Trent, S. Lilly Zheng, Jianfeng Xu, Zengnan Mo

Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

Yann S. Dufour, Saheed Imam, Byoung-Mo Koo, Heather A. Green, Timothy J. Donohue

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans

Fan Liu, Fedde van der Lijn, Claudia Schurmann, Gu Zhu, M. Mallar Chakravarty, Pirro G. Hysi, Andreas Wollstein, Oscar Lao, Marleen de Bruijne, M. Arfan Ikram, Aad van der Lugt, Fernando Rivadeneira, André G. Uitterlinden, Albert Hofman, Wiro J. Niessen, Georg Homuth, Greig de Zubicaray, Katie L. McMahon, Paul M. Thompson, Amro Daboul, Ralf Puls, Katrin Hegenscheid, Liisa Bevan, Zdenka Pausova, Sarah E. Medland, Grant W. Montgomery, Margaret J. Wright, Carol Wicking, Stefan Boehringer, Timothy D. Spector, Tomáš Paus, Nicholas G. Martin, Reiner Biffar, Manfred Kayser

H4K20me1 Contributes to Downregulation of X-Linked Genes for C. elegans Dosage Compensation

Anne Vielle, Jackie Lang, Yan Dong, Sevinc Ercan, Chitra Kotwaliwale, Andreas Rechtsteiner, Alex Appert, Q. Brent Chen, Andrea Dose, Thea Egelhofer, Hiroshi Kimura, Przemyslaw Stempor, Abby Dernburg, Jason D. Lieb, Susan Strome, Julie Ahringer

Citrullination of Histone H3 Interferes with HP1-Mediated Transcriptional Repression

Priyanka Sharma, Saliha Azebi, Patrick England, Tove Christensen, Anné Møller-Larsen, Thor Petersen, Eric Batsché, Christian Muchardt

Transcriptional Repression of Hox Genes by C. elegans HP1/HPL and H1/HIS-24

Maja Studencka, Radosław Wesołowski, Lennart Opitz, Gabriela Salinas-Riester, Jacek R. Wisniewski, Monika Jedrusik-Bode

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

Chen Xie, Yong E. Zhang, Jia-Yu Chen, Chu-Jun Liu, Wei-Zhen Zhou, Ying Li, Mao Zhang, Rongli Zhang, Liping Wei, Chuan-Yun Li

C. elegans SIRT6/7 Homolog SIR-2.4 Promotes DAF-16 Relocalization and Function during Stress

Wei-Chung Chiang, Daniel X. Tishkoff, Bo Yang, Joshua Wilson-Grady, Xiaokun Yu, Travis Mazer, Mark Eckersdorff, Steven P. Gygi, David B. Lombard, Ao-Lin Hsu

Functional Variants in NFKBIE and RTKN2 Involved in Activation of the NF-κB Pathway Are Associated with Rheumatoid Arthritis in Japanese

Keiko Myouzen, Yuta Kochi, Yukinori Okada, Chikashi Terao, Akari Suzuki, Katsunori Ikari, Tatsuhiko Tsunoda, Atsushi Takahashi, Michiaki Kubo, Atsuo Taniguchi, Fumihiko Matsuda, Koichiro Ohmura, Shigeki Momohara, Tsuneyo Mimori, Hisashi Yamanaka, Naoyuki Kamatani, Ryo Yamada, Yusuke Nakamura, Kazuhiko Yamamoto

Integrative Genomic Analysis Identifies Isoleucine and CodY as Regulators of Listeria monocytogenes Virulence

Lior Lobel, Nadejda Sigal, Ilya Borovok, Eytan Ruppin, Anat A. Herskovits

Rare Copy Number Variants Contribute to Congenital Left-Sided Heart Disease

Marc-Phillip Hitz, Louis-Philippe Lemieux-Perreault, Christian Marshall, Yassamin Feroz-Zada, Robbie Davies, Shi Wei Yang, Anath Christopher Lionel, Guylaine D'Amours, Emmanuelle Lemyre, Rebecca Cullum, Jean-Luc Bigras, Maryse Thibeault, Philippe Chetaille, Alexandre Montpetit, Paul Khairy, Bert Overduin, Sabine Klaassen, Pamela Hoodless, Mona Nemer, Alexandre F. R. Stewart, Cornelius Boerkoel, Stephen W. Scherer, Andrea Richter, Marie-Pierre Dubé, Gregor Andelfinger

Normal DNA Methylation Dynamics in DICER1-Deficient Mouse Embryonic Stem Cells

Jonathan Ip, Paul Canham, K. H. Andy Choo, Yoshimi Inaba, Shelley A. Jacobs, Paul Kalitsis, Deidre M. Mattiske, Jane Ng, Richard Saffery, Nicholas C. Wong, Lee H. Wong, Jeffrey R. Mann

Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

Dai-Yin Chao, Adriano Silva, Ivan Baxter, Yu S. Huang, Magnus Nordborg, John Danku, Brett Lahner, Elena Yakubova, David E. Salt