Publications from 2010
AATF mediates an antiapoptotic effect of the unfolded protein response through transcriptional regulation of AKT1, Shinsuke Ishigaki, Sonya G. Fonseca, Christine M. Oslowski, Agata Jurczyk, Jeffrey R. Shearstone, Lihua Julie Zhu, M. A. Permutt, Dale L. Greiner, Fumihiko Urano, and Rita Bortell
A novel role for the centrosomal protein, pericentrin, in regulation of insulin secretory vesicle docking in mouse pancreatic beta-cells, Agata Jurczyk, Steven C. Pino, Bryan O'Sullivan-Murphy, Martha Addorio, Erich A. Lidstone, Philip diLorio, Kathryn L. Lipson, Clive Standley, Kevin E. Fogarty, Lawrence M. Lifshitz, Fumihiko Urano, John P. Mordes, Dale L. Greiner, Aldo A. Rossini, and Rita Bortell
Mediator and cohesin connect gene expression and chromatin architecture, Michael H. Kagey, Jamie J. Newman, Steve Bilodeau, Ye Zhan, David A. Orlando, Nynke L. van Berkum, Christopher C. Ebmeier, Jesse Goossens, Peter B. Rahl, Stuart S. Levine, Dylan J. Taatjes, Job Dekker, and Richard A. Young
Chromatin as a potential carrier of heritable information, Paul D. Kaufman and Oliver J. Rando
Sister cohesion and structural axis components mediate homolog bias of meiotic recombination, Keun P. Kim, Beth M. Weiner, Liangran Zhang, Amy Jordan, Job Dekker, and Nancy Kleckner
Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone, Erin M. Kolonko, Brittany N. Albaugh, Scott E. Lindner, Yuanyuan Chen, Kenneth A. Satyshur, Kevin M. Arnold, Paul D. Kaufman, James G. Keck, and John M. Denu
A new DAF-16 isoform regulates longevity, Eun-Soo Kwon, Sri Devi Narasimhan, Kelvin Yen, and Heidi A. Tissenbaum
Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis., Jessica Lopes da Rosa Spiegler, Victor L. Boyartchuk, Lihua Julie Zhu, and Paul D. Kaufman
Proliferating cell nuclear antigen (PCNA) is required for cell cycle-regulated silent chromatin on replicated and nonreplicated genes, Andrew Miller, Jiji Chen, Taichi E. Takasuka, Jennifer L. Jacobi, Paul D. Kaufman, Joseph M.K. Irudayaraj, and Ann L. Kirchmaier
Integrating one-dimensional and three-dimensional maps of genomes, Natalia Naumova and Job Dekker
MicroRNA-mediated integration of haemodynamics and Vegf signalling during angiogenesis, Stefania Nicoli, Clive Standley, Paul Walker, Adam Hurlstone, Kevin E. Fogarty, and Nathan D. Lawson
A switch from life to death in endoplasmic reticulum stressed beta-cells, Christine M. Oslowski and Fumihiko Urano
The binary switch between life and death of endoplasmic reticulum-stressed beta cells, Christine M. Oslowski and Fumihiko Urano
The binary switch that controls the life and death decisions of ER stressed beta cells, Christine M. Oslowski and Fumihiko Urano
A genome-wide RNA interference screen reveals an essential CREB3L2-ATF5-MCL1 survival pathway in malignant glioma with therapeutic implications, Zhi Sheng, Li Li, Lihua Julie Zhu, Thomas W. Smith, Andrea Demers, Alonzo H. Ross, Richard P. Moser, and Michael R. Green
The U2AF35-related protein Urp contacts the 3' splice site to promote U12-type intron splicing and the second step of U2-type intron splicing, Haihong Shen, Xuexiu Zheng, Stephan Luecke, and Michael R. Green
Maternal Rnf12/RLIM is required for imprinted X-chromosome inactivation in mice, JongDae Shin, Michael Bossenz, Young Chung, Hong Ma, Meg Byron, Naoko Taniguchi-Ishigaki, Xiaochun Zhu, Jiao Baowei, Lisa L. Hall, Michael R. Green, Stephen N. Jones, Irm Hermans-Borgmeyer, Jeanne B. Lawrence, and Ingolf Bach
Hi-C: a method to study the three-dimensional architecture of genomes, Nynke L. van Berkum, Erez Lieberman-Aiden, Louise Williams, Maxim Imakaev, Andreas Gnirke, Leonid A. Mirny, Job Dekker, and Eric S. Lander
Genomics tools for unraveling chromosome architecture, Bas van Steensel and Job Dekker
Role for IGFBP7 in senescence induction by BRAF, Narendra Wajapeyee, Ryan W. Serra, Xiaochun Zhu, Meera Mahalingam, and Michael R. Green
Role for IGFBP7 in senescence induction by BRAF., Narendra Wajapeyee, Ryan W. Serra, Xiaochun Zhu, Meera Mahalingam, and Michael R. Green
Senescence induction in human fibroblasts and hematopoietic progenitors by leukemogenic fusion proteins., Narendra Wajapeyee, Shu-Zong Wang, Ryan W. Serra, Peter D. Solomon, Arvindhan Nagarajan, Xiaochun Zhu, and Michael R. Green
PPARs: diverse regulators in energy metabolism and metabolic diseases, Yong-Xu Wang
Rescue of HIV-1 Release by Targeting Widely Divergent NEDD4-Type Ubiquitin Ligases and Isolated Catalytic HECT Domains to Gag, Eric R. Weiss, Elena Popova, Hikaru Yamanaka, Hyung Cheol Kim, Jon M. Huibregtse, and Heinrich G. Göttlinger
A comparative study of fat storage quantitation in nematode Caenorhabditis elegans using label and label-free methods, Kelvin Yen, Thuc T. Le, Ankita Bansal, Sri Devi Narasimhan, Ji-Xin Cheng, and Heidi A. Tissenbaum
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data, Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Herve Pages, Simon M. Lin, David S. Lapointe, and Michael R. Green
Publications from 2009
A Versatile Viral System for Expression and Depletion of Proteins in Mammalian Cells, Eric Campeau, Victoria E. Ruhl, Francis Rodier, Corey Lewis Smith, Brittany L. Rahmberg, Jill O. Fuss, Judith Campisi, Paul Yaswen, Priscilla K. Cooper, and Paul D. Kaufman
Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization, Howard Y. Chang, Olivier Cuvier, and Job Dekker
Differential roles of insulin-like growth factor receptor- and insulin receptor-mediated signaling in the phenotypes of hepatocellular carcinoma cells, Ya-Wen Chen, Victor L. Boyartchuk, and Brian C. Lewis
A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development, Laurence D. Covassin, Arndt F. Siekmann, Michael C. Kacergis, Elizabeth Laver, John C. Moore, Jacques A. Villefranc, Brant M. Weinstein, and Nathan D. Lawson
Ceramide kinase regulates phospholipase C and phosphatidylinositol 4, 5, bisphosphate in phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun, Ikuko Yonamine, Satinder S. Rawat, Raghavendra Pralhada Rao, Kunio Nagashima, Eiichiro Fukusaki, Vishwajeet Puri, Patrick J. Dolph, Petra Schwille, Jairaj K. Acharya, and Usha Acharya
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening, Barbara D'haene, Catia Attanasio, Diane Beysen, Josee Dostie, Edmond Lemire, Philippe Bouchard, Michael Field, Kristie Jones, Birgit Lorenz, Bjorn Menten, Karen Buysse, Filip Pattyn, Marc Friedli, Catherine Ucla, Colette Rossier, Carine Wyss, Frank Speleman, Anne De Paepe, Job Dekker, Stylianos E. Antonarakis, and Elfride De Baere
A negatively charged residue in place of histone H3K56 supports chromatin assembly factor association but not genotoxic stress resistance, Judith A. Erkmann and Paul D. Kaufman
Endoplasmic reticulum stress in beta-cells and development of diabetes, Sonya G. Fonseca, Mark Burcin, Jesper Gromada, and Fumihiko Urano
A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors, Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, and Albertha J. M. Walhout
Selective interaction between Trf3 and Taf3 required for early development and hematopoiesis, Daniel O. Hart, Manas K. Santra, Tamal Raha, and Michael R. Green
Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer, Steven A. Johnsen, Cenap Gungor, Tanja Prenzel, Sabine Riethdorf, Lutz Riethdorf, Naoko Taniguchi-Ishigaki, Thomas Rau, Baris Tursun, J. David Furlow, Guido Sauter, Martin Scheffner, Klaus Pantel, Frank Gannon, and Ingolf Bach
Valproate, a mood stabilizer, induces WFS1 expression and modulates its interaction with ER stress protein GRP94, Chihiro Kakiuchi, Shinsuke Ishigaki, Christine M. Oslowski, Sonya G. Fonseca, Tadafumi Kato, and Fumihiko Urano
Runx2 induces acute myeloid leukemia in cooperation with Cbfbeta-SMMHC in mice, Ya-Huei Kuo, Sayyed K. Zaidi, Svetlana Gornostaeva, Toshihisa Komori, Gary S. Stein, and Lucio H. Castilla
My5C: web tools for chromosome conformation capture studies, Bryan R. Lajoie, Nynke L. van Berkum, Amartya Sanyal, and Job Dekker
Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Berstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John A. Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, and Job Dekker
The interplay between transcription factors and microRNAs in genome-scale regulatory networks, Natalia Julia Martinez and Albertha J. M. Walhout
Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions, Adriana Miele, Kerstin Bystricky, and Job Dekker
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C), Adriana Miele and Job Dekker
InAKTivation of insulin/IGF-1 signaling by dephosphorylation., Sri Devi Narasimhan, Arnab Mukhopadhyay, and Heidi A. Tissenbaum
Converging pathways in lifespan regulation., Sri Devi Narasimhan, Kelvin Yen, and Heidi A. Tissenbaum
Annotating the human genome with Disease Ontology, John D. Osborne, Jared M. Flatow, Michelle Holko, Simon M. Lin, Warren A. Kibbe, Lihua Julie Zhu, Maria I. Danila, Gang Feng, and Rex L. Chisholm
Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery, Pranav O. Oza, Sue L. Jaspersen, Adriana Miele, Job Dekker, and Craig L. Peterson
A PP2A regulatory subunit regulates C. elegans insulin/IGF-1 signaling by modulating AKT-1 phosphorylation., Srivatsan Padmanabhan, Arnab Mukhopadhyay, Sri Devi Narasimhan, Gregory J. Tesz, Michael P. Czech, and Heidi A. Tissenbaum
Epigenetic silencing of the RASSF1A tumor suppressor gene through HOXB3-mediated induction of DNMT3B expression, Rajendra Kumar Palakurthy, Narendra Wajapeyee, Manas K. Santra, Claude Gazin, Ling Lin, Stephane Gobeil, and Michael R. Green
Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas, Michael J. Parsons, Harshan Pisharath, Shamila Yusuff, John C. Moore, Arndt F. Siekmann, Nathan D. Lawson, and Steven D. Leach
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors, John S. Reece-Hoyes, Bart Deplancke, M. Inmaculada Barrasa, Julia Hatzold, Ryan B. Smit, H. Efsun Arda, Patricia A. Pope, Jeb Gaudet, Barbara Conradt, and Albertha J. M. Walhout
F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage, Manas K. Santra, Narendra Wajapeyee, and Michael R. Green
Transcription and signalling pathways involved in BCR-ABL-mediated misregulation of 24p3 and 24p3R, Zhi Sheng, Shu-Zong Wang, and Michael R. Green
Chemokine signaling guides regional patterning of the first embryonic artery, Arndt F. Siekmann, Clive Standley, Kevin E. Fogarty, Scot A. Wolfe, and Nathan D. Lawson
Determining spatial chromatin organization of large genomic regions using 5C technology, Nynke L. van Berkum and Job Dekker
Efficacy of IGFBP7 for treatment of metastatic melanoma and other cancers in mouse models and human cell lines, Narendra Wajapeyee, Varun Kapoor, Meera Mahalingam, and Michael R. Green
Getting an edge on human disease, Albertha J. M. Walhout
Mitochondrial degeneration and not apoptosis is the primary cause of embryonic lethality in ceramide transfer protein mutant mice, Xin Wang, Raghavendra Pralhada Rao, Teresa Kosakowska-Cholody, M. Athar Masood, Eileen Southon, Helin Zhang, Cyril Berthet, Kunio Nagashima, Timothy K. Veenstra, Lino Tessarollo, Usha Acharya, and Jairaj K. Acharya
Identification of a protein, G0S2, that lacks Bcl-2 homology domains and interacts with and antagonizes Bcl-2, Christian Welch, Manas K. Santra, Wissal El-Assaad, Xiaochun Zhu, Wade E. Huber, Richard A. Keys, Jose G. Teodoro, and Michael R. Green
Nuclear factor-kappaB-mediated transforming growth factor-beta-induced expression of vimentin is an independent predictor of biochemical recurrence after radical prostatectomy, Qiang Zhang, Brian T. Helfand, Thomas L. Jang, Lihua Julie Zhu, Lin Chen, Ximing J. Yang, James Kozlowski, Norm Smith, Shilajit Kundu, Guangyu Yang, Adekunle A. Raji, Borko Javonovic, Michael Pins, Paul Lindholm, Yinglu Guo, William J. Catalona, and Chung Lee
Publications from 2008
Cell-nonautonomous function of ceramidase in photoreceptor homeostasis, Jairaj K. Acharya, Ujjaini Dasgupta, Satinder S. Rawat, Changqing Yuan, Parthena D. Sanxaridis, Ikuko Yonamine, Pusha Karim, Kunio Nagashima, Michael H. Brodsky, Susan Tsunoda, and Usha Acharya
RTEL1 maintains genomic stability by suppressing homologous recombination, Louise J. Barber, Jillian L. Youds, Jordan D. Ward, Michael J. McIlwraith, Nigel J. O'Neil, Mark I.R. Petalcorin, Julie S. Martin, Spencer J. Collis, Sharon B. Cantor, Melissa M. Auclair, Heidi A. Tissenbaum, Stephen C. West, Ann M. Rose, and Simon J. Boulton
Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75, Christopher E. Berndsen, Toshiaki Tsubota, Scott E. Lindner, Susan Lee, James M. Holton, Paul D. Kaufman, James G. Keck, and John M. Denu
Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes, Mugdha Bhati, Christopher Lee, Amy L. Nancarrow, Mihwa Lee, Vanessa J. Craig, Ingolf Bach, J. Mitchell Guss, Joel P. Mackay, and Jacqueline M. Matthews
C/EBPalpha in leukemogenesis: a matter of being in the right place with the right signals, Lucio H. Castilla
The role of nitric oxide and the unfolded protein response in cytokine-induced beta-cell death, Kari T. Chambers, Julie A. Unverferth, Sarah M. Weber, Ronald C. Wek, Fumihiko Urano, and John A. Corbett
p19Arf inhibits the invasion of hepatocellular carcinoma cells by binding to C-terminal binding protein, Ya-Wen Chen, Seema Paliwal, Kyle M. Draheim, Steven R. Grossman, and Brian C. Lewis
Gene regulation in the third dimension, Job Dekker
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
Transcription factor functionality and transcription regulatory networks, Christian A. Grove and Albertha J. M. Walhout
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
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
The role of IRE1alpha in the degradation of insulin mRNA in pancreatic beta-cells, Kathryn L. Lipson, Rajarshi Ghosh, and Fumihiko Urano
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
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
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
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
Long-range chromosomal interactions and gene regulation, Angela Miele and Job Dekker
Trp53 deletion stimulates the formation of metastatic pancreatic tumors, Jennifer P. Morton, David S. Klimstra, Michelle E. Mongeau, and Brian C. Lewis
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
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
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
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
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
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
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
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
Mapping networks of physical interactions between genomic elements using 5C technology, Josee Dostie and Job Dekker
Chromosome conformation capture carbon copy technology, Josee Dostie, Ye Zhan, and Job Dekker
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
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
Endoplasmic reticulum stress signaling in pancreatic beta-cells, Sonya G. Fonseca, Kathryn L. Lipson, and Fumihiko Urano
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
An elaborate pathway required for Ras-mediated epigenetic silencing, Claude Gazin, Narendra Wajapeyee, Stephane Gobeil, Ching-man A. Virbasius, and Michael R. Green
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
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
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