Publications from 2007
Dorfin-CHIP chimeric proteins potently ubiquitylate and degrade familial ALS-related mutant SOD1 proteins and reduce their cellular toxicity, Shinsuke Ishigaki, Jun-ichi Niwa, Shin-ichi Yamada, Miho Takahashi, Takashi Ito, Jun Sone, Manabu Doyu, Fumihiko Urano, and Gen Sobue
Cbfbeta-SMMHC impairs differentiation of common lymphoid progenitors and reveals an essential role for RUNX in early B-cell development, Ya-Huei Kuo, Rachel M. Gerstein, and Lucio H. Castilla
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex, Chiara Lanzuolo, Virginie Roure, Job Dekker, Frederic Bantignies, and Valerio Orlando
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method, Xiangdong Meng, Stacey Thibodeau-Beganny, Tao Jiang, J. Keith Joung, and Scot A. Wolfe
Shh signaling and pancreatic cancer: implications for therapy, Jennifer P. Morton and Brian C. Lewis
Sonic hedgehog acts at multiple stages during pancreatic tumorigenesis, Jennifer P. Morton, Michelle E. Mongeau, David S. Klimstra, John P. Morris, Yie Chia Lee, Yoshiya Kawaguchi, Christopher V. E. Wright, Matthias Hebrok, and Brian C. Lewis
An endocytic pathway as a target of tubby for regulation of fat storage, Arnab Mukhopadhyay, Xiaojing Pan, David G. Lambright, and Heidi A. Tissenbaum
Reproduction and longevity: secrets revealed by C. elegans, Arnab Mukhopadhyay and Heidi A. Tissenbaum
The alternative reading frame tumor suppressor antagonizes hypoxia-induced cancer cell migration via interaction with the COOH-terminal binding protein corepressor, Seema Paliwal, Ramesh C. Kovi, Bharath D. Nath, Ya-Wen Chen, Brian C. Lewis, and Steven R. Grossman
Ceramide transfer protein function is essential for normal oxidative stress response and lifespan, Raghavendra Pralhada Rao, Changqing Yuan, Jeremy C. Allegood, Satinder S. Rawat, Michael Beth Edwards, Xin Wang, Alfred H. Merrill Jr., Usha Acharya, and Jairaj K. Acharya
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns, John S. Reece-Hoyes, Jane Shingles, Denis Dupuy, Christian A. Grove, Albertha J. M. Walhout, Marc Vidal, and Ian A. Hope
Light-induced recruitment of INAD-signaling complexes to detergent-resistant lipid rafts in Drosophila photoreceptors, Parthena D. Sanxaridis, Michelle A. Cronin, Satinder S. Rawat, Girma Waro, Usha Acharya, and Susan Tsunoda
RS domain-splicing signal interactions in splicing of U12-type and U2-type introns, Haihong Shen and Michael R. Green
Notch signalling limits angiogenic cell behaviour in developing zebrafish arteries, Arndt F. Siekmann and Nathan D. Lawson
Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes, Toshiaki Tsubota, Christopher E. Berndsen, Judith A. Erkmann, Corey Lewis Smith, Lanhao Yang, Michael A. Freitas, John M. Denu, and Paul D. Kaufman
Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network, Vanessa Vermeirssen, M. Inmaculada Barrasa, Cesar A. Hidalgo, Jenny Aurielle B. Babon, Reynaldo Sequerra, Lynn Doucette-Stamm, Albert-Laszlo Barabasi, and Albertha J. M. Walhout
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping, Vanessa Vermeirssen, Bart Deplancke, M. Inmaculada Barrasa, John S. Reece-Hoyes, H. Efsun Arda, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, Michael R. Brent, and Albertha J. M. Walhout
Gateway compatible vectors for analysis of gene function in the zebrafish, Jacques A. Villefranc, Julio D. Amigo, and Nathan D. Lawson
Genetic variation in Mon1a affects protein trafficking and modifies macrophage iron loading in mice, Fudi Wang, Prasad N. Paradkar, Angel O. Custodio, Diane McVey Ward, Mark D. Fleming, Dean Campagna, Kristina A. Roberts, Victor L. Boyartchuk, William F. Dietrich, Jerry Kaplan, and Nancy C. Andrews
CBFB-MYH11 hinders early T-cell development and induces massive cell death in the thymus, Ling Zhao, Jennifer Cannons, Stacie Anderson, Martha Kirby, Liping Xu, Lucio H. Castilla, Pamela L. Schwartzberg, Remy Bosselut, and P. Paul Liu
Publications from 2006
Drosophila melanogaster Scramblases modulate synaptic transmission, Usha Acharya, Michael Beth Edwards, Ramon A. Jorquera, Hugo Silva, Kunio Nagashima, Pedro Labarca, and Jairaj K. Acharya
Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics, Andrew J. Antczak, Toshiaki Tsubota, Paul D. Kaufman, and James M. Berger
Global analysis of hematopoietic and vascular endothelial gene expression by tissue specific microarray profiling in zebrafish, Laurence D. Covassin, Julio D. Amigo, Kana Suzuki, Viktor Teplyuk, Juerg R. Straubhaar, and Nathan D. Lawson
Distinct genetic interactions between multiple Vegf receptors are required for development of different blood vessel types in zebrafish, Laurence D. Covassin, Jacques A. Villefranc, Michael C. Kacergis, Brant M. Weinstein, and Nathan D. Lawson
The three 'C' s of chromosome conformation capture: controls, controls, controls, Job Dekker
A gene-centered C. elegans protein-DNA interaction network, Bart Deplancke, Arnab Mukhopadhyay, Wanyuan Ao, Ahmed M. Elewa, Christian A. Grove, Natalia Julia Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, John S. Reece-Hoyes, Ian A. Hope, Heidi A. Tissenbaum, Susan E. Mango, and Albertha J. M. Walhout
Gateway-Compatible Yeast One-Hybrid Screens, Bart Deplancke, Vanessa Vermeirssen, H. Efsun Arda, Albertha J. M. Walhout, and Natalia Julia Martinez
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements, Josee Dostie, Todd A. Richmond, Ramy A. Arnaout, Rebecca R. Selzer, William L. Lee, Tracey A. Honan, Eric D. Rubio, Anton Krumm, Justin Lamb, Chad Nusbaum, Roland D. Green, and Job Dekker
Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1, Davide Gabellini, Giuseppe D'Antona, Maurizio Moggio, Alessandro Prelle, Chiara Zecca, Raffaella Adami, Barbara Angeletti, Patrizia Ciscato, Maria Antonietta Pellegrino, Roberto Bottinelli, Michael R. Green, and Rossella Tupler
Listeria monocytogenes as a probe of immune function, Oleg Garifulin and Victor L. Boyartchuk
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications, Nele Gheldof, Tomoko M. Tabuchi, and Job Dekker
Apoptin nucleocytoplasmic shuttling is required for cell type-specific localization, apoptosis, and recruitment of the anaphase-promoting complex/cyclosome to PML bodies, Destin W. Heilman, Jose G. Teodoro, and Michael R. Green
Cbfbeta reduces Cbfbeta-SMMHC-associated acute myeloid leukemia in mice, Susan Ann Heilman, Ya-Huei Kuo, Chantal S. Goudswaard, Peter J. Valk, and Lucio H. Castilla
Cbf beta-SMMHC induces distinct abnormal myeloid progenitors able to develop acute myeloid leukemia, Ya-Huei Kuo, Sean F. Landrette, Susan Ann Heilman, Paola N. Perrat, Lisa Garrett, Pu P. Liu, Michelle M. Le Beau, Scott C. Kogan, and Lucio H. Castilla
Development of the pancreas and pancreatic cancer, Brian C. Lewis
Regulation of insulin biosynthesis in pancreatic beta cells by an endoplasmic reticulum-resident protein kinase IRE1, Kathryn L. Lipson, Sonya G. Fonseca, Shinsuke Ishigaki, Linh X. Nguyen, Elizabeth Foss, Rita Bortell, Aldo A. Rossini, and Fumihiko Urano
Endoplasmic reticulum stress-induced apoptosis and auto-immunity in diabetes, Kathryn L. Lipson, Sonya G. Fonseca, and Fumihiko Urano
Counter-selectable marker for bacterial-based interaction trap systems, Xiangdong Meng, Robin M. Smith, Astrid V. Giesecke, J. Keith Joung, and Scot A. Wolfe
Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system, Xiangdong Meng and Scot A. Wolfe
Mapping chromatin interactions by chromosome conformation capture, Adriana Miele, Nele Gheldof, Tomoko M. Tabuchi, Josee Dostie, and Job Dekker
Worming pathways to and from DAF-16/FOXO, Arnab Mukhopadhyay, Seung Wook Oh, and Heidi A. Tissenbaum
Autophagy is activated for cell survival after endoplasmic reticulum stress, Maiko Ogata, Shin-ichiro Hino, Atsushi Saito, Keisuke Morikawa, Shinichi Kondo, Soshi Kanemoto, Tomohiko Murakami, Manabu Taniguchi, Ichiro Tanii, Kazuya Yoshinaga, Sadao Shiosaka, James A. Hammarback, Fumihiko Urano, and Kazunori Imaizumi
Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation, Seung Wook Oh, Arnab Mukhopadhyay, Bharat L. Dixit, Tamal Raha, Michael R. Green, and Heidi A. Tissenbaum
Epigenetic telomere protection by Drosophila DNA damage response pathways, Sarah R. Oikemus, Joana Queiroz-Machado, KuanJu Lai, Nadine Schultz, Claudio E. Sunkel, and Michael H. Brodsky
Dynamic expression of LIM cofactors in the developing mouse neural tube, Heather P. Ostendorff, Baris Tursun, Kerstin Cornils, Anne Schluter, Alexander Drung, Cenap Gungor, and Ingolf Bach
Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis, J. Recht, Toshiaki Tsubota, J. C. Tanny, R. L. Diaz, James M. Berger, X. Zhang, B. A. Garcia, J. Shabanowitz, A. L. Burlingame, D. F. Hunt, Paul D. Kaufman, and C. David Allis
A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks, John S. Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A. Grove, Ian A. Hope, and Albertha J. M. Walhout
RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans, Haihong Shen and Michael R. Green
p53-mediated inhibition of angiogenesis through up-regulation of a collagen prolyl hydroxylase, Jose G. Teodoro, Albert E. Parker, Xiaochun Zhu, and Michael R. Green
Networking at the second Interactome Meeting, Albertha J. M. Walhout
Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping, Albertha J. M. Walhout
Biochemistry and Molecular Biology, Albertha J. M. Walhout and Simon J. Boulton
C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO, Yamei Wang, Seung Wook Oh, Bart Deplancke, Jianyuan Luo, Albertha J. M. Walhout, and Heidi A. Tissenbaum
Overlapping and distinct functions for a Caenorhabditis elegans SIR2 and DAF-16/FOXO, Yamei Wang and Heidi A. Tissenbaum
Publications from 2005
Enzymes of sphingolipid metabolism in Drosophila melanogaster, Usha Acharya and Jairaj K. Acharya
lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein, Ewa M. Davison, Melissa M. Harrison, Albertha J. M. Walhout, Marc Vidal, and H. Robert Horvitz
A cell-surface receptor for lipocalin 24p3 selectively mediates apoptosis and iron uptake, Laxminarayana R. Devireddy, Claude Gazin, Xiaochun Zhu, and Michael R. Green
WFS1 is a novel component of the unfolded protein response and maintains homeostasis of the endoplasmic reticulum in pancreatic beta-cells, Sonya G. Fonseca, Mariko Fukuma, Kathryn L. Lipson, Linh X. Nguyen, Jenny R. Allen, Yoshitomo Oka, and Fumihiko Urano
Histone deposition proteins: links between the DNA replication machinery and epigenetic gene silencing, Alexa A. Franco and Paul D. Kaufman
Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C, Alexa A. Franco, Wendy M. Lam, Peter M. Burgers, and Paul D. Kaufman
Bloom syndrome ortholog HIM-6 maintains genomic stability in C. elegans, Melissa M. Grabowski, Nenad Svrzikapa, and Heidi A. Tissenbaum
Replication-independent histone deposition by the HIR complex and Asf1, Erin M. Green, Andrew J. Antczak, Aaron O. Bailey, Alexa A. Franco, Kevin J. Wu, John R. Yates III, and Paul D. Kaufman
The anaphase promoting complex: a critical target for viral proteins and anti-cancer drugs, Destin W. Heilman, Michael R. Green, and Jose G. Teodoro
XBP1 activates the transcription of its target genes via an ACGT core sequence under ER stress, Soshi Kanemoto, Shinichi Kondo, Maiko Ogata, Tomohiko Murakami, Fumihiko Urano, and Kazunori Imaizumi
Fluoride induces endoplasmic reticulum stress in ameloblasts responsible for dental enamel formation, Kaori Kubota, Daniel H. Lee, Masahiro Tsuchiya, Conan S. Young, Eric T. Everett, Esperanza A. Martinez-Mier, Malcolm Snead, Linh X. Nguyen, Fumihiko Urano, and John D. Bartlett
The absence of p53 promotes metastasis in a novel somatic mouse model for hepatocellular carcinoma, Brian C. Lewis, David S. Klimstra, Nicholas D. Socci, Su Xu, Jason A. Koutcher, and Harold E. Varmus
A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors, Xiangdong Meng, Michael H. Brodsky, and Scot A. Wolfe
C. elegans tubby regulates life span and fat storage by two independent mechanisms, Arnab Mukhopadhyay, Bart Deplancke, Albertha J. M. Walhout, and Heidi A. Tissenbaum
JNK regulates lifespan in Caenorhabditis elegans by modulating nuclear translocation of forkhead transcription factor/DAF-16, Seung Wook Oh, Arnab Mukhopadhyay, Nenad Svrzikapa, Feng Jiang, Roger J. Davis, and Heidi A. Tissenbaum
HIV-1 Tat stimulates transcription complex assembly through recruitment of TBP in the absence of TAFs, Tamal Raha, S. W. Grace Cheng, and Michael R. Green
Regulation of histone deposition proteins Asf1/Hir1 by multiple DNA damage checkpoint kinases in Saccharomyces cerevisiae, Judith A. Sharp, Gizem Rizki, and Paul D. Kaufman
The ubiquitin ligase Rnf6 regulates local LIM kinase 1 levels in axonal growth cones, Baris Tursun, Anne Schluter, Marvin A. Peters, Birte Viehweger, Heather P. Ostendorff, Juliana Soosairajah, Alexander Drung, Michael Bossenz, Steven A. Johnsen, Michaela Schweizer, Ora Bernard, and Ingolf Bach
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1, Christopher R. Vakoc, Danielle L. Letting, Nele Gheldof, Tomoyuki Sawado, M. A. Bender, Mark Groudine, Mitchell J. Weiss, Job Dekker, and Gerd A. Blobel
Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA, Rugang Zhang, Maxim V. Poustovoitov, Xiaofen Ye, Hidelita A. Santos, Wei Chen, Sally M. Daganzo, Jan P. Erzberger, Ilya G. Serebriiskii, Adrian A. Canutescu, Roland L. Dunbrack, John R. Pehrson, James M. Berger, Paul D. Kaufman, and Peter D. Adams
Publications from 2004
Ceramidase expression facilitates membrane turnover and endocytosis of rhodopsin in photoreceptors, Usha Acharya, Michael Beth Mowen, Kunio Nagashima, and Jairaj K. Acharya
High ER stress in beta-cells stimulates intracellular degradation of misfolded insulin, Jenny R. Allen, Linh X. Nguyen, Karen E.G. Sargent, Kathryn L. Lipson, Anthony Hackett, and Fumihiko Urano
In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer, Sukesh R. Bhaumik, Tamal Raha, David P. Aiello, and Michael R. Green
The host resistance locus sst1 controls innate immunity to Listeria monocytogenes infection in immunodeficient mice, Victor L. Boyartchuk, Mauricio Rojas, Bo-Shiun Yan, Ousman Jobe, Nicholas Hurt, David M. Dorfman, Darren E. Higgins, William F. Dietrich, and Igor Kramnik
Drosophila melanogaster MNK/Chk2 and p53 regulate multiple DNA repair and apoptotic pathways following DNA damage, Michael H. Brodsky, Brian T. Weinert, Garson Tsang, Yikang S. Rong, Nadine Schultz, Kent G. Golic, Donald C. Rio, and Gerald M. Rubin
Identification of genes that synergize with Cbfb-MYH11 in the pathogenesis of acute myeloid leukemia, Lucio H. Castilla, Paola N. Perrat, Natalia Julia Martinez, Sean F. Landrette, R. Keys, Sarah R. Oikemus, J. Flanegan, Susan Ann Heilman, Lisa Garrett, A. Dutra, S. Anderson, German A. Pihan, L. Wolff, and Pu P. Liu
A gateway-compatible yeast one-hybrid system, Bart Deplancke, Denis Dupuy, Marc Vidal, and Albertha J. M. Walhout
A first version of the Caenorhabditis elegans Promoterome, Denis Dupuy, Qian-Ru Li, Bart Deplancke, Mike Boxem, Tong Hao, Philippe Lamesch, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Ian A. Hope, David E. Hill, Albertha J. M. Walhout, and Marc Vidal
PPARs and the complex journey to obesity, Ronald M. Evans, Grant D. Barrish, and Yong-Xu Wang
When enough is enough: genetic diseases associated with transcriptional derepression, Davide Gabellini, Michael R. Green, and Rossella Tupler
Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5, Ridgely Fisk Green, Monique A. Lorson, Albertha J. M. Walhout, Marc Vidal, and Sander van den Heuvel
Evidence for dynamically organized modularity in the yeast protein-protein interaction network, Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. M. Walhout, Michael E. Cusick, Frederick P. Roth, and Marc Vidal
Amyloid beta induces neuronal cell death through ROS-mediated ASK1 activation, H. Kadowaki, H. Nishitoh, Fumihiko Urano, C. Sadamitsu, A. Matsuzawa, K. Takeda, H. Masutani, J. Yodoi, Y. Urano, T. Nagano, and H. Ichijo
U2AF homology motifs: protein recognition in the RRM world, Clara L. Kielkopf, Stephan Lucke, and Michael R. Green
A mechanical basis for chromosome function, Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, and John N. Hutchinson
Plag1 and Plagl2 are oncogenes that induce acute myeloid leukemia in cooperation with Cbfb-MYH11, Sean F. Landrette, Ya-Huei Kuo, Karen Hensen, Sahar Barjesteh van Waalwijk van Doorn-Khosrovani, Paola N. Perrat, Wim J. M. Van de Ven, Ruud Delwel, and Lucio H. Castilla
Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation, Bertrand Molle, Stephane Pere, Vieri Failli, Ingolf Bach, and Sylvie Retaux
Drosophila atm/telomere fusion is required for telomeric localization of HP1 and telomere position effect, Sarah R. Oikemus, Nadine Schultz, Joana Queiroz-Machado, Hanna Tukachinsky, Saeko Takada, Claudio E. Sunkel, and Michael H. Brodsky
A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly, Haihong Shen and Michael R. Green
A single polypyrimidine tract binding protein (PTB) binding site mediates splicing inhibition at mouse IgM exons M1 and M2, Haihong Shen, Julie L. C. Kan, Claudia Ghigna, Giuseppe Biamonti, and Michael R. Green
Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly, Haihong Shen, Julie L. C. Kan, and Michael R. Green
The viral protein Apoptin associates with the anaphase-promoting complex to induce G2/M arrest and apoptosis in the absence of p53, Jose G. Teodoro, Destin W. Heilman, Albert E Parker, and Michael R. Green
[Stress signaling from the endoplasmic reticulum], Fumihiko Urano
Regulation of muscle fiber type and running endurance by PPARdelta, Yong-Xu Wang, Chung-Li Zhang, Ruth T. Yu, Helen K. Cho, Michael C. Nelson, Corinne R. Bayuga-Ocampo, Jungyeob Ham, Heonjoong Kang, and Ronald M. Evans
Compartment-specific perturbation of protein handling activates genes encoding mitochondrial chaperones, Takunari Yoneda, Cristina Benedetti, Fumihiko Urano, Scott G. Clark, Heather P. Harding, and David Ron
Publications from 2003
Integrating 'omic' information: a bridge between genomics and systems biology, Hui Ge, Albertha J. M. Walhout, and Marc Vidal