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 2008

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Gene regulation in the third dimension, Job Dekker

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Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction, Job Dekker

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A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene, Stephane Gobeil, Xiaochun Zhu, Charles J. Doillon, and Michael R. Green

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Transcription factor functionality and transcription regulatory networks, Christian A. Grove and Albertha J. M. Walhout

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Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast, Tommy Kaplan, Chih Long Liu, Judith A. Erkmann, John Holik, Michael Grunstein, Paul D. Kaufman, Nir Friedman, and Oliver J. Rando

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A mechanism for Ikaros regulation of human globin gene switching, Janelle R. Keys, Michael R. Tallack, Ye Zhan, Peter Papathanasiou, Christopher Goodnow, Karin M. Gaensler, Merlin Crossley, Job Dekker, and Andrew C. Perkins

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The role of IRE1alpha in the degradation of insulin mRNA in pancreatic beta-cells, Kathryn L. Lipson, Rajarshi Ghosh, and Fumihiko Urano

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AIP1 is critical in transducing IRE1-mediated endoplasmic reticulum stress response, Dianhong Luo, Yun He, Haifeng Zhang, Luyang Yu, Hong Chen, Zhe Xu, Shibo Tang, Fumihiko Urano, and Wang Min

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A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity, Natalia Julia Martinez, Maria C. Ow, M. Inmaculada Barrasa, Molly Hammell, Reynaldo Sequerra, Lynn Doucette-Stamm, Frederick P. Roth, Victor R. Ambros, and Albertha J. M. Walhout

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Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity, Natalia Julia Martinez, Maria C. Ow, John S. Reece-Hoyes, M. Inmaculada Barrasa, Victor R. Ambros, and Albertha J. M. Walhout

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Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases, Xiangdong Meng, Marcus Blaine Noyes, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe

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Long-range chromosomal interactions and gene regulation, Angela Miele and Job Dekker

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Trp53 deletion stimulates the formation of metastatic pancreatic tumors, Jennifer P. Morton, David S. Klimstra, Michelle E. Mongeau, and Brian C. Lewis

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Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans, Arnab Mukhopadhyay, Bart Deplancke, Albertha J. M. Walhout, and Heidi A. Tissenbaum

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Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites, Marcus Blaine Noyes, Ryan G. Christensen, Atsuya Wakabayashi, Gary D. Stormo, Michael H. Brodsky, and Scot A. Wolfe

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The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans, Maria C. Ow, Natalia Julia Martinez, Philip H. Olsen, Howard S. Silverman, M. Inmaculada Barrasa, Barbara Conradt, Albertha J. M. Walhout, and Victor R. Ambros

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Protein kinase C signaling during T cell activation induces the endoplasmic reticulum stress response, Steven C. Pino, Bryan O'Sullivan-Murphy, Erich A. Lidstone, Thomas B. Thornley, Agata Jurczyk, Fumihiko Urano, Dale L. Greiner, John P. Mordes, Aldo A. Rossini, and Rita Bortell

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Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome, Haihong Shen, Xuexiu Zheng, Jingping Shen, Lingdi Zhang, Rui Zhao, and Michael R. Green

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Aneuploidy: cells losing their balance, Eduardo M. Torres, Bret R. Williams, and Angelika Amon

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Oncogenic BRAF induces senescence and apoptosis through pathways mediated by the secreted protein IGFBP7, Narendra Wajapeyee, Ryan W. Serra, Xiaochun Zhu, Meera Mahalingam, and Michael R. Green

Publications from 2007

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EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression, M. Inmaculada Barrasa, Philippe Vaglio, Fabien Cavasino, Laurent Jacotot, and Albertha J. M. Walhout

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Loss of p53 and Ink4a/Arf cooperate in a cell autonomous fashion to induce metastasis of hepatocellular carcinoma cells, Ya-Wen Chen, David S. Klimstra, Michelle E. Mongeau, Jessica L. Tatem, Victor L. Boyartchuk, and Brian C. Lewis

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GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p, Job Dekker

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Mapping networks of physical interactions between genomic elements using 5C technology, Josee Dostie and Job Dekker

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Chromosome conformation capture carbon copy technology, Josee Dostie, Ye Zhan, and Job Dekker

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Assessing tumor progression factors by somatic gene transfer into a mouse model: Bcl-xL promotes islet tumor cell invasion, Yi-Chieh Nancy Du, Brian C. Lewis, Douglas Hanahan, and Harold E. Varmus

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, ENCODE Project Consortium, Zhiping Weng, and Job Dekker

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Endoplasmic reticulum stress signaling in pancreatic beta-cells, Sonya G. Fonseca, Kathryn L. Lipson, and Fumihiko Urano

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Irf3 polymorphism alters induction of interferon beta in response to Listeria monocytogenes infection, Oleg Garifulin, Zanmei Qi, Haihong Shen, Sujatha Patnala, Michael R. Green, and Victor L. Boyartchuk

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An elaborate pathway required for Ras-mediated epigenetic silencing, Claude Gazin, Narendra Wajapeyee, Stephane Gobeil, Ching-man A. Virbasius, and Michael R. Green

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Proteasomal selection of multiprotein complexes recruited by LIM homeodomain transcription factors, Cenap Gungor, Naoko Taniguchi-Ishigaki, Hong Ma, Alexander Drung, Baris Tursun, Heather P. Ostendorff, Michael Bossenz, Catherina G. Becker, Thomas Becker, and Ingolf Bach

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Quantitative analysis of chromosome conformation capture assays (3C-qPCR), Helene Hagege, Petra Klous, Caroline Braem, Erik Splinter, Job Dekker, Guy Cathala, Wouter de Laat, and Thierry Forne

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Initiation of zebrafish haematopoiesis by the TATA-box-binding protein-related factor Trf3, Daniel O. Hart, Tamal Raha, Nathan D. Lawson, and Michael R. Green

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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

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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

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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

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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

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Shh signaling and pancreatic cancer: implications for therapy, Jennifer P. Morton and Brian C. Lewis

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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

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An endocytic pathway as a target of tubby for regulation of fat storage, Arnab Mukhopadhyay, Xiaojing Pan, David G. Lambright, and Heidi A. Tissenbaum

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Reproduction and longevity: secrets revealed by C. elegans, Arnab Mukhopadhyay and Heidi A. Tissenbaum

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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

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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

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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

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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

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RS domain-splicing signal interactions in splicing of U12-type and U2-type introns, Haihong Shen and Michael R. Green

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Notch signalling limits angiogenic cell behaviour in developing zebrafish arteries, Arndt F. Siekmann and Nathan D. Lawson

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Effects of aneuploidy on cellular physiology and cell division in haploid yeast, Eduardo M. Torres, Tanya Sokolsky, Cheryl M. Tucker, Leon Y. Chan, Monica Boselli, Maitreya J. Dunham, and Angelika Amon

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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

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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

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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

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Gateway compatible vectors for analysis of gene function in the zebrafish, Jacques A. Villefranc, Julio D. Amigo, and Nathan D. Lawson

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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

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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

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Drosophila melanogaster Scramblases modulate synaptic transmission, Usha Acharya, Michael Beth Edwards, Ramon A. Jorquera, Hugo Silva, Kunio Nagashima, Pedro Labarca, and Jairaj K. Acharya

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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

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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

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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

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The three 'C' s of chromosome conformation capture: controls, controls, controls, Job Dekker

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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

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Gateway-Compatible Yeast One-Hybrid Screens, Bart Deplancke, Vanessa Vermeirssen, H. Efsun Arda, Albertha J. M. Walhout, and Natalia Julia Martinez

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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

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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

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Listeria monocytogenes as a probe of immune function, Oleg Garifulin and Victor L. Boyartchuk

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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

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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

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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

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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

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Development of the pancreas and pancreatic cancer, Brian C. Lewis

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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

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Endoplasmic reticulum stress-induced apoptosis and auto-immunity in diabetes, Kathryn L. Lipson, Sonya G. Fonseca, and Fumihiko Urano

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Counter-selectable marker for bacterial-based interaction trap systems, Xiangdong Meng, Robin M. Smith, Astrid V. Giesecke, J. Keith Joung, and Scot A. Wolfe

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Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system, Xiangdong Meng and Scot A. Wolfe

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Mapping chromatin interactions by chromosome conformation capture, Adriana Miele, Nele Gheldof, Tomoko M. Tabuchi, Josee Dostie, and Job Dekker

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Worming pathways to and from DAF-16/FOXO, Arnab Mukhopadhyay, Seung Wook Oh, and Heidi A. Tissenbaum

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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

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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

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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

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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

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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

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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