This collection showcases the journal articles, book chapters, and other publications and presentations written by faculty and researchers of the Program in Gene Function and Expression (PGFE) at the University of Massachusetts Medical School.

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Publications from 2006

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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

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RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans, Haihong Shen and Michael R. Green

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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

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Protein-tyrosine kinase and GTPase signals cooperate to phosphorylate and activate Wiskott-Aldrich syndrome protein (WASP)/neuronal WASP, Eduardo M. Torres and Michael K. Rosen

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Networking at the second Interactome Meeting, Albertha J. M. Walhout

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Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping, Albertha J. M. Walhout

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Biochemistry and Molecular Biology, Albertha J. M. Walhout and Simon J. Boulton

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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

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Overlapping and distinct functions for a Caenorhabditis elegans SIR2 and DAF-16/FOXO, Yamei Wang and Heidi A. Tissenbaum

Publications from 2005

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Enzymes of sphingolipid metabolism in Drosophila melanogaster, Usha Acharya and Jairaj K. Acharya

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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

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A cell-surface receptor for lipocalin 24p3 selectively mediates apoptosis and iron uptake, Laxminarayana R. Devireddy, Claude Gazin, Xiaochun Zhu, and Michael R. Green

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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

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Histone deposition proteins: links between the DNA replication machinery and epigenetic gene silencing, Alexa A. Franco and Paul D. Kaufman

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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

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Bloom syndrome ortholog HIM-6 maintains genomic stability in C. elegans, Melissa M. Grabowski, Nenad Svrzikapa, and Heidi A. Tissenbaum

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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

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The anaphase promoting complex: a critical target for viral proteins and anti-cancer drugs, Destin W. Heilman, Michael R. Green, and Jose G. Teodoro

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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

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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

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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

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A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors, Xiangdong Meng, Michael H. Brodsky, and Scot A. Wolfe

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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

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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

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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

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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

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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

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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

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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

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Ceramidase expression facilitates membrane turnover and endocytosis of rhodopsin in photoreceptors, Usha Acharya, Michael Beth Mowen, Kunio Nagashima, and Jairaj K. Acharya

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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

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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

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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

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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

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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

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A gateway-compatible yeast one-hybrid system, Bart Deplancke, Denis Dupuy, Marc Vidal, and Albertha J. M. Walhout

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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

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PPARs and the complex journey to obesity, Ronald M. Evans, Grant D. Barrish, and Yong-Xu Wang

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When enough is enough: genetic diseases associated with transcriptional derepression, Davide Gabellini, Michael R. Green, and Rossella Tupler

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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

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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

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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

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U2AF homology motifs: protein recognition in the RRM world, Clara L. Kielkopf, Stephan Lucke, and Michael R. Green

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A mechanical basis for chromosome function, Nancy Kleckner, Denise Zickler, Gareth H. Jones, Job Dekker, Ruth Padmore, Jim Henle, and John N. Hutchinson

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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

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Lhx9 and lhx9alpha: differential biochemical properties and effects on neuronal differentiation, Bertrand Molle, Stephane Pere, Vieri Failli, Ingolf Bach, and Sylvie Retaux

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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

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A pathway of sequential arginine-serine-rich domain-splicing signal interactions during mammalian spliceosome assembly, Haihong Shen and Michael R. Green

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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

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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

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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

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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

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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

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Integrating 'omic' information: a bridge between genomics and systems biology, Hui Ge, Albertha J. M. Walhout, and Marc Vidal

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A conserved amphipathic helix in WASP/Scar proteins is essential for activation of Arp2/3 complex, Sanjay C. Panchal, Donald A. Kaiser, Eduardo M. Torres, Thomas D. Pollard, and Michael K. Rosen

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Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs), Stephan P. Persengiev, Xiaochun Zhu, and Michael R. Green

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Contingent phosphorylation/dephosphorylation provides a mechanism of molecular memory in WASP, Eduardo M. Torres and Michael K. Rosen

Publications from 2002

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Integrated version of reverse two-hybrid system for the postproteomic era, Hideki Endoh, Sylvie Vincent, Yves Jacob, Eleonore Real, Albertha J. M. Walhout, and Marc Vidal

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MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans, Nancy N. Huang, Darcy E. Mootz, Albertha J. M. Walhout, Marc Vidal, and Craig P. Hunter

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Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline, Albertha J. M. Walhout, Jerome Reboul, Olena Shtanko, Nicolas Bertin, Philippe Vaglio, Hui Ge, Hongmei Lee, Lynn Doucette-Stamm, Kristin C. Gunsalus, Aaron J. Schetter, Diane G. Morton, Kenneth J. Kemphues, Valerie Reinke, Stuart K. Kim, Fabio Piano, and Marc Vidal

Publications from 2001

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A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome, Anne Davy, Paul Bello, Nicolas Thierry-Mieg, Philippe Vaglio, Joseph Hitti, Lynn Doucette-Stamm, Danielle Thierry-Mieg, Jerome Reboul, Simon J. Boulton, Albertha J. M. Walhout, Olivier Coux, and Marc Vidal

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High-throughput yeast two-hybrid assays for large-scale protein interaction mapping, Albertha J. M. Walhout and Marc Vidal

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Protein interaction maps for model organisms, Albertha J. M. Walhout and Marc Vidal

Publications from 2000

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A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions, Hideki Endoh, Albertha J. M. Walhout, and Marc Vidal

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Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm, Albertha J. M. Walhout, Simon J. Boulton, and Marc Vidal

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GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes, Albertha J. M. Walhout, Gary F. Temple, Michael A. Brasch, James L. Hartley, Monique A. Lorson, Sander van den Heuvel, and Marc Vidal

Publications from 1999

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Protein interaction mapping in C. elegans using proteins involved in vulval development, Albertha J. M. Walhout, Raffaella Sordella, Xiaowei Lu, James L. Hartley, Gary F. Temple, Michael A. Brasch, Nicolas Thierry-Mieg, and Marc Vidal

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A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens, Albertha J. M. Walhout and Marc Vidal

Publications from 1998

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A model of elegance, Albertha J. M. Walhout, Hideki Endoh, Nicolas Thierry-Mieg, Wendy Wong, and Marc Vidal

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Sequences flanking the E-box contribute to cooperative binding by c-Myc/Max heterodimers to adjacent binding sites, Albertha J. M. Walhout, P. C. van der Vliet, and H. Th. M. Timmers

Publications from 1997

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The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis, M. R. Gunner, Emil Alexov, Eduardo M. Torres, and Samir Lipovaca

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c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene, Albertha J. M. Walhout, J. M. Gubbels, R. Bernards, P. C. van der Vliet, and H. Th. M. Timmers

Publications from 1993

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E1A functions as a coactivator of retinoic acid-dependent retinoic acid receptor-beta 2 promoter activation, Frank A. E. Kruyt, Gert E. Folkers, Albertha J. M. Walhout, Bas-jan M. van der Leede, and Paul T. van der Saag