An empirical framework for binary interactome mapping (2009)
Venkatesan, Kavitha, Rual, Jean-Francois, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets....
Shifted Transversal Design smart-pooling for high coverage interactome mapping (2009)
Xin, Xiaofeng, Rual, Jean-François, Hirozane-Kishikawa, Tomoko, Hill, David E., Vidal, Marc, Boone, Charles, ...
“Smart-pooling,” in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level...
Ozanick, Sarah G., Wang, Xuying, Costanzo, Michael, Brost, Renee L., Boone, Charles, Anderson, James T.
A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of...
344 Review TRENDS in Cell Biology Vol.13 No.7 July 2003 (2008)
Gary D. Bader, Adrian Heilbut, Brenda Andrews, Mike Tyers, Timothy Hughes, Charles Boone
Functional genomics and proteomics: charting a multidimensional map of the yeast cell q
A Specificity Map for the PDZ Domain Family (2008)
Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
Ainslie B. Parsons, Andres Lopez, Inmar E. Givoni, David E. Williams, Christopher A. Gray, Raymond J. Andersen, ...
Discovering target and off-target effects of specific compounds is critical to drug discovery and development. We generated a compendium of ‘‘chemical-genetic interaction’ ’ profiles by...
808 RESEARCH ARTICLE Global Mapping of the Yeast Genetic Interaction Network (2008)
Amy Hin, Yan Tong, Guillaume Lesage, Gary D. Bader, Huiming Ding, Hong Xu, ...
A genetic interaction network containing �1000 genes and �4000 interactions was mapped by crossing mutations in 132 different query genes into a set of �4700 viable gene yeast deletion mutants...
Musso, Gabriel, Costanzo, Michael, Huangfu, ManQin, Smith, Andrew M., Paw, Jadine, San Luis, Bryan-Joseph, ...
Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence...
Identification of a novel lysophospholipid acyltransferase in Saccharomyces cerevisiae (2007)
Shilpa, Jain, Stanford, NaTaza, Bhagwat, Neha, Seiler, Brian, Costanzo, Michael, Boone, Charles, ...
The incorporation of unsaturated acyl chains into phospholipids during de novo synthesis is primarily mediated by the 1-acylsn- glycerol-3-phosphate acyltransferase reaction. In S. cerevisiae, Slc1...
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions....
A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability (2005)
Budd, Martin E., Tong, Amy Hin Yan, Polaczek, Piotr, Peng, Xiao, Boone, Charles, Campbell, Judith L.
To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately...
A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability (2005)
Martin E. Budd, Piotr Polaczek, Xiao Peng, Charles Boone, Judith L. Campbell
To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately...
A Network of Multi-tasking Proteins at the DNA replication Fork Preserves Genome Stability (2005)
Martin E. Budd, Piotr Polaczek, Xiao Peng, Charles Boone, Judith Campbell
Synthetic lethal screens in yeast have been carried out primarily using non-essential genes as queries. To elucidate the network that maintains high fidelity genome replication, we have introduced...
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiaeinteraction network (2005)
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
Abstract Background Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence...
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae (2005)
Lesage, Guillaume, Shapiro, Jesse, Specht, Charles A, Sdicu, Anne-Marie, Ménard, Patrice, Hussein, Shamiza, ...
Abstract Background In S. cerevisiae the β-1,4-linked N-acetylglucosamine polymer, chitin, is synthesized by a family of 3 specialized but interacting chitin synthases encoded by CHS1 , CHS2 and...
Maya Schuldiner, Sean R. Collins, Natalie J. Thompson, Vladimir Denic, Arunashree Bhamidipati, Thanuja Punna, ...
We present a strategy for generating and analyzing comprehensive genetic-interaction maps, termed E-MAPs (epistatic miniarray profiles), comprising quantitative measures of aggravating or alleviating...
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae (2005)
Lesage, Guillaume, Shapiro, Jesse, Specht, Charles, Sdicu, Anne-Marie, Ménard, Patrice, Hussein, Shamiza, ...
BACKGROUND:In S. cerevisiae the ß-1,4-linked N-acetylglucosamine polymer, chitin, is synthesized by a family of 3 specialized but interacting chitin synthases encoded by CHS1, CHS2 and CHS3. Chs2p...
Zhang, Lan, King, Oliver, Wong, Sharyl, Goldberg, Debra, Tong, Amy, Lesage, Guillaume, ...
BACKGROUND:Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology,...
Chang, Michael, Bellaoui, Mohammed, Boone, Charles, Brown, Grant W.
We performed a systematic screen of the set of ≈5,000 viable Saccharomyces cerevisiae haploid gene deletion mutants and have identified 103 genes whose deletion causes sensitivity to the...
Goehring, April S., Mitchell, David A., Tong, Amy Hin Yan, Keniry, Megan E., Boone, Charles, Sprague, George F.
The p21-activated kinases Ste20p and Cla4p carry out undefined functions that are essential for viability during budding in Saccharomyces cerevisiae. To gain insight into the roles of Ste20p, we have...
Elg1 forms an alternative RFC complex important for DNA replication and genome integrity
Bellaoui, Mohammed, Chang, Michael, Ou, Jiongwen, Xu, Hong, Boone, Charles, Brown, Grant W.
Genome-wide synthetic genetic interaction screens with mutants in the mus81 and mms4 replication fork-processing genes identified a novel replication factor C (RFC) homolog, Elg1, which forms an...
Kozminski, Keith G., Beven, Laure, Angerman, Elizabeth, Tong, Amy Hin Yan, Boone, Charles, Park, Hay-Oak
Polarized cell growth requires the coupling of a defined spatial site on the cell cortex to the apparatus that directs the establishment of cell polarity. In the budding yeast Saccharomyces...
Identification of Protein Complexes Required for Efficient Sister Chromatid Cohesion
Mayer, Melanie L., Pot, Isabelle, Chang, Michael, Xu, Hong, Aneliunas, Victoria, Kwok, Teresa, ...
Ctf8p is a component of Ctf18-RFC, an alternative replication factor C-like complex required for efficient sister chromatid cohesion in Saccharomyces cerevisiae. We performed synthetic genetic array...
Krogan, Nevan J., Kim, Minkyu, Tong, Amy, Golshani, Ashkan, Cagney, Gerard, Canadien, Veronica, ...
Set2 methylates Lys36 of histone H3. We show here that yeast Set2 copurifies with RNA polymerase II (RNAPII). Chromatin immunoprecipitation analyses demonstrated that Set2 and histone H3 Lys36...
Measday, Vivien, Baetz, Kristin, Guzzo, Julie, Yuen, Karen, Kwok, Teresa, Sheikh, Bilal, ...
Accurate chromosome segregation requires the execution and coordination of many processes during mitosis, including DNA replication, sister chromatid cohesion, and attachment of chromosomes to...
Mrc1 Is Required for Sister Chromatid Cohesion To Aid in Recombination Repair of Spontaneous Damage
Xu, Hong, Boone, Charles, Klein, Hannah L.
The SRS2 gene of Saccharomyces cerevisiae encoding a 3′→5′ DNA helicase is part of the postreplication repair pathway and functions to ensure proper repair of DNA damage arising during DNA...
Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton
Audhya, Anjon, Loewith, Robbie, Parsons, Ainslie B, Gao, Lu, Tabuchi, Mitsuaki, Zhou, Huilin, ...
To further understand the roles played by the essential phosphoinositide PI4,5P2, we have used a synthetic lethal analysis, which systematically combined the mss4ts mutation, partially defective in...
Combining biological networks to predict genetic interactions
Wong, Sharyl L., Zhang, Lan V., Tong, Amy H. Y., Li, Zhijian, Goldberg, Debra S., King, Oliver D., ...
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism...
Sciorra, Vicki A., Audhya, Anjon, Parsons, Ainslie B., Segev, Nava, Boone, Charles, Emr, Scott D.
Phosphorylated derivatives of phosphatidylinositol are essential regulators of both endocytic and exocytic trafficking in eukaryotic cells. In Saccharomyces cerevisiae, the phosphatidylinositol...
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
Lesage, Guillaume, Shapiro, Jesse, Specht, Charles A, Sdicu, Anne-Marie, Ménard, Patrice, Hussein, Shamiza, ...
Chang, Michael, Bellaoui, Mohammed, Zhang, Chaoying, Desai, Ridhdhi, Morozov, Pavel, Delgado-Cruzata, Lissette, ...
SGS1 encodes a DNA helicase whose homologues in human cells include the BLM, WRN, and RECQ4 genes, mutations in which lead to cancer-predisposition syndromes. Clustering of synthetic genetic...
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability
Budd, Martin E, Tong, Amy Hin Yan, Polaczek, Piotr, Peng, Xiao, Boone, Charles, Campbell, Judith L
To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately...
High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants.
Jorgensen, Paul, Nelson, Bryce, Robinson, Mark D, Chen, Yiqun, Andrews, Brenda, Tyers, Mike, ...
We present a method for high-resolution genetic mapping that takes advantage of the ordered set of viable gene deletion mutants, which form a set of colinear markers covering almost every centimorgan...
Anderson, James B, Sirjusingh, Caroline, Parsons, Ainslie B, Boone, Charles, Wickens, Claire, Cowen, Leah E, ...
We show that mode of selection, degree of dominance of mutations, and ploidy are determining factors in the evolution of resistance to the antifungal drug fluconazole in yeast. In experiment 1, yeast...
Nelson, Bryce, Parsons, Ainslie B, Evangelista, Marie, Schaefer, Karen, Kennedy, Kathy, Ritchie, Steven, ...
Cell fusion in the budding yeast Saccharomyces cerevisiae is a temporally and spatially regulated process that involves degradation of the septum, which is composed of cell wall material, and occurs...
Suter, Bernhard, Tong, Amy, Chang, Michael, Yu, Lisa, Brown, Grant W, Boone, Charles, ...
Mutations in genes encoding the origin recognition complex (ORC) of Saccharomyces cerevisiae affect initiation of DNA replication and transcriptional repression at the silent mating-type loci. To...
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Tabuchi, Mitsuaki, Audhya, Anjon, Parsons, Ainslie B., Boone, Charles, Emr, Scott D.
The Stt4 phosphatidylinositol 4-kinase has been shown to generate a pool of phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, critical for actin cytoskeleton organization and cell...
Chang, Michael, Bellaoui, Mohammed, Boone, Charles, Brown, Grant W.
We performed a systematic screen of the set of ≈5,000 viable Saccharomyces cerevisiae haploid gene deletion mutants and have identified 103 genes whose deletion causes sensitivity to the...
Goehring, April S., Mitchell, David A., Tong, Amy Hin Yan, Keniry, Megan E., Boone, Charles, Sprague, George F.
The p21-activated kinases Ste20p and Cla4p carry out undefined functions that are essential for viability during budding in Saccharomyces cerevisiae. To gain insight into the roles of Ste20p, we have...
Elg1 forms an alternative RFC complex important for DNA replication and genome integrity
Bellaoui, Mohammed, Chang, Michael, Ou, Jiongwen, Xu, Hong, Boone, Charles, Brown, Grant W.
Genome-wide synthetic genetic interaction screens with mutants in the mus81 and mms4 replication fork-processing genes identified a novel replication factor C (RFC) homolog, Elg1, which forms an...
Kozminski, Keith G., Beven, Laure, Angerman, Elizabeth, Tong, Amy Hin Yan, Boone, Charles, Park, Hay-Oak
Polarized cell growth requires the coupling of a defined spatial site on the cell cortex to the apparatus that directs the establishment of cell polarity. In the budding yeast Saccharomyces...
Identification of Protein Complexes Required for Efficient Sister Chromatid Cohesion
Mayer, Melanie L., Pot, Isabelle, Chang, Michael, Xu, Hong, Aneliunas, Victoria, Kwok, Teresa, ...
Ctf8p is a component of Ctf18-RFC, an alternative replication factor C-like complex required for efficient sister chromatid cohesion in Saccharomyces cerevisiae. We performed synthetic genetic array...
Krogan, Nevan J., Kim, Minkyu, Tong, Amy, Golshani, Ashkan, Cagney, Gerard, Canadien, Veronica, ...
Set2 methylates Lys36 of histone H3. We show here that yeast Set2 copurifies with RNA polymerase II (RNAPII). Chromatin immunoprecipitation analyses demonstrated that Set2 and histone H3 Lys36...
Mrc1 Is Required for Sister Chromatid Cohesion To Aid in Recombination Repair of Spontaneous Damage
Xu, Hong, Boone, Charles, Klein, Hannah L.
The SRS2 gene of Saccharomyces cerevisiae encoding a 3′→5′ DNA helicase is part of the postreplication repair pathway and functions to ensure proper repair of DNA damage arising during DNA...
Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton
Audhya, Anjon, Loewith, Robbie, Parsons, Ainslie B, Gao, Lu, Tabuchi, Mitsuaki, Zhou, Huilin, ...
To further understand the roles played by the essential phosphoinositide PI4,5P2, we have used a synthetic lethal analysis, which systematically combined the mss4ts mutation, partially defective in...
Combining biological networks to predict genetic interactions
Wong, Sharyl L., Zhang, Lan V., Tong, Amy H. Y., Li, Zhijian, Goldberg, Debra S., King, Oliver D., ...
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism...
Sciorra, Vicki A., Audhya, Anjon, Parsons, Ainslie B., Segev, Nava, Boone, Charles, Emr, Scott D.
Phosphorylated derivatives of phosphatidylinositol are essential regulators of both endocytic and exocytic trafficking in eukaryotic cells. In Saccharomyces cerevisiae, the phosphatidylinositol...
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
Lesage, Guillaume, Shapiro, Jesse, Specht, Charles A, Sdicu, Anne-Marie, Ménard, Patrice, Hussein, Shamiza, ...
Chang, Michael, Bellaoui, Mohammed, Zhang, Chaoying, Desai, Ridhdhi, Morozov, Pavel, Delgado-Cruzata, Lissette, ...
SGS1 encodes a DNA helicase whose homologues in human cells include the BLM, WRN, and RECQ4 genes, mutations in which lead to cancer-predisposition syndromes. Clustering of synthetic genetic...
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
Measday, Vivien, Baetz, Kristin, Guzzo, Julie, Yuen, Karen, Kwok, Teresa, Sheikh, Bilal, ...
Accurate chromosome segregation requires the execution and coordination of many processes during mitosis, including DNA replication, sister chromatid cohesion, and attachment of chromosomes to...
A Network of Multi-Tasking Proteins at the DNA Replication Fork Preserves Genome Stability
Budd, Martin E, Tong, Amy Hin Yan, Polaczek, Piotr, Peng, Xiao, Boone, Charles, Campbell, Judith L
To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately...
High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants.
Jorgensen, Paul, Nelson, Bryce, Robinson, Mark D, Chen, Yiqun, Andrews, Brenda, Tyers, Mike, ...
We present a method for high-resolution genetic mapping that takes advantage of the ordered set of viable gene deletion mutants, which form a set of colinear markers covering almost every centimorgan...
Anderson, James B, Sirjusingh, Caroline, Parsons, Ainslie B, Boone, Charles, Wickens, Claire, Cowen, Leah E, ...
We show that mode of selection, degree of dominance of mutations, and ploidy are determining factors in the evolution of resistance to the antifungal drug fluconazole in yeast. In experiment 1, yeast...
Nelson, Bryce, Parsons, Ainslie B, Evangelista, Marie, Schaefer, Karen, Kennedy, Kathy, Ritchie, Steven, ...
Cell fusion in the budding yeast Saccharomyces cerevisiae is a temporally and spatially regulated process that involves degradation of the septum, which is composed of cell wall material, and occurs...
Suter, Bernhard, Tong, Amy, Chang, Michael, Yu, Lisa, Brown, Grant W, Boone, Charles, ...
Mutations in genes encoding the origin recognition complex (ORC) of Saccharomyces cerevisiae affect initiation of DNA replication and transcriptional repression at the silent mating-type loci. To...
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Tabuchi, Mitsuaki, Audhya, Anjon, Parsons, Ainslie B., Boone, Charles, Emr, Scott D.
The Stt4 phosphatidylinositol 4-kinase has been shown to generate a pool of phosphatidylinositol 4-phosphate (PI4P) at the plasma membrane, critical for actin cytoskeleton organization and cell...
Identifying transcription factor functions and targets by phenotypic activation
Chua, Gordon, Morris, Quaid D., Sopko, Richelle, Robinson, Mark D., Ryan, Owen, Chan, Esther T., ...
Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes...
Hurto, Rebecca L., Tong, Amy Hin Yan, Boone, Charles, Hopper, Anita K.
Nuclear export of tRNA is an essential eukaryotic function, yet the one known yeast tRNA nuclear exporter, Los1, is nonessential. Moreover recent studies have shown that tRNAs can move retrograde...
Gao, Xiang-Dong, Sperber, Lauren M., Kane, Steven A., Tong, Zongtian, Tong, Amy Hin Yan, Boone, Charles, ...
Polarization of cell growth along a defined axis is essential for the generation of cell and tissue polarity. In the budding yeast Saccharomyces cerevisiae, Axl2p plays an essential role in...
Genetic Dissection of Parallel Sister-Chromatid Cohesion Pathways
Xu, Hong, Boone, Charles, Brown, Grant W.
Sister-chromatid cohesion, the process of pairing replicated chromosomes during mitosis and meiosis, is mediated through the essential cohesin complex and a number of nonessential cohesion genes, but...
Ohkuni, Kentaro, Abdulle, Rashid, Tong, Amy Hin Yan, Boone, Charles, Kitagawa, Katsumi
The spindle checkpoint ensures the accurate segregation of chromosomes by monitoring the status of kinetochore attachment to microtubules. Simultaneous mutations in one of several kinetochore and...
Gillingham, Alison K., Tong, Amy Hin Yan, Boone, Charles, Munro, Sean
Rud3p is a coiled-coil protein of the yeast cis-Golgi. We find that Rud3p is localized to the Golgi via a COOH-terminal domain that is distantly related to the GRIP domain that recruits several...
Alto, Neal M., Weflen, Andrew W., Rardin, Matthew J., Yarar, Defne, Lazar, Cheri S., Tonikian, Raffi, ...
Bacterial toxins and effector proteins hijack eukaryotic enzymes that are spatially localized and display rapid signaling kinetics. However, the molecular mechanisms by which virulence factors engage...
Amaro, I. Alexandra, Costanzo, Michael, Boone, Charles, Huffaker, Tim C.
Stu1 is the Saccharomyces cerevisiae member of the CLASP family of microtubule plus-end tracking proteins and is essential for spindle formation. A genomewide screen for gene deletions that are...
Anderson, Blake L., Boldogh, Istvan, Evangelista, Marie, Boone, Charles, Greene, Lloyd A., Pon, Liza A.
The budding yeast contains two type I myosins, Myo3p and Myo5p, with redundant functions. Deletion of both myosins results in growth defects, loss of actin polarity and polarized cell surface growth,...
Control of Mitotic Spindle Position by the Saccharomyces cerevisiae Formin Bni1p
Lee, Laifong, Klee, Saskia K., Evangelista, Marie, Boone, Charles, Pellman, David
Alignment of the mitotic spindle with the axis of cell division is an essential process in Saccharomyces cerevisiae that is mediated by interactions between cytoplasmic microtubules and the cell...
A Role for Myosin-I in Actin Assembly through Interactions with Vrp1p, Bee1p, and the Arp2/3 Complex
Evangelista, Marie, Klebl, Bert M., Tong, Amy H.Y., Webb, Bradley A., Leeuw, Thomas, Leberer, Ekkehard, ...
Type I myosins are highly conserved actin-based molecular motors that localize to the actin-rich cortex and participate in motility functions such as endocytosis, polarized morphogenesis, and cell...
A protein interaction map for cell polarity development
Drees, Becky L., Sundin, Bryan, Brazeau, Elizabeth, Caviston, Juliane P., Chen, Guang-Chao, Guo, Wei, ...
Many genes required for cell polarity development in budding yeast have been identified and arranged into a functional hierarchy. Core elements of the hierarchy are widely conserved, underlying cell...
Willis, Ian M., Chua, Gordon, Tong, Amy H., Brost, Renee L., Hughes, Timothy R., Boone, Charles, ...
Transcriptional repression of ribosomal components and tRNAs is coordinately regulated in response to a wide variety of environmental stresses. Part of this response involves the convergence of...
Zhao, Rongmin, Kakihara, Yoshito, Gribun, Anna, Huen, Jennifer, Yang, Guocheng, Khanna, May, ...
Hsp90 is a highly conserved molecular chaperone that is involved in modulating a multitude of cellular processes. In this study, we identify a function for the chaperone in RNA processing and...
A Specificity Map for the PDZ Domain Family
Tonikian, Raffi, Zhang, Yingnan, Sazinsky, Stephen L, Currell, Bridget, Yeh, Jung-Hua, Reva, Boris, ...
PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides,...
Federovitch, Christine M., Jones, Ying Z., Tong, Amy H., Boone, Charles, Prinz, William A., Hampton, Randolph Y.
The endoplasmic reticulum (ER) is highly plastic, and increased expression of distinct single ER-resident membrane proteins, such as HMG-CoA reductase (HMGR), can induce a dramatic restructuring of...
Yu, Lisa, Lopez, Andres, Anaflous, Abderrahmane, El Bali, Brahim, Hamal, Abdellah, Ericson, Elke, ...
Small molecules have been shown to be potent and selective probes to understand cell physiology. Here, we show that imidazo[1,2-a]pyridines and imidazo[1,2-a]pyrimidines compose a class of compounds...
Mousley, Carl J., Tyeryar, Kimberly, Ile, Kristina E., Schaaf, Gabriel, Brost, Renee L., Boone, Charles, ...
Synthetic genetic array analyses identify powerful genetic interactions between a thermosensitive allele (sec14-1ts) of the structural gene for the major yeast phosphatidylinositol transfer protein...
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
Musso, Gabriel, Costanzo, Michael, Huangfu, ManQin, Smith, Andrew M., Paw, Jadine, San Luis, Bryan-Joseph, ...
Since complete redundancy between extant duplicates (paralogs) is evolutionarily unfavorable, some degree of functional congruency is eventually lost. However, in budding yeast, experimental evidence...
Ozanick, Sarah G., Wang, Xuying, Costanzo, Michael, Brost, Renee L., Boone, Charles, Anderson, James T.
A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of...
Dixon, Scott J., Fedyshyn, Yaroslav, Koh, Judice L. Y., Prasad, T. S. Keshava, Chahwan, Charly, Chua, Gordon, ...
Synthetic lethal genetic interaction networks define genes that work together to control essential functions and have been studied extensively in Saccharomyces cerevisiae using the synthetic genetic...
Exploring the conservation of synthetic lethal genetic interaction networks
Dixon, Scott J, Andrews, Brenda J, Boone, Charles
High-throughput studies have enabled the large-scale mapping of synthetic lethal genetic interaction networks in the budding yeast Saccharomyces cerevisiae (S. cerevisiae). Recently, complementary...
The interaction network of the chaperonin CCT
Dekker, Carien, Stirling, Peter C, McCormack, Elizabeth A, Filmore, Heather, Paul, Angela, Brost, Renee L, ...
The eukaryotic cytosolic chaperonin containing TCP-1 (CCT) has an important function in maintaining cellular homoeostasis by assisting the folding of many proteins, including the cytoskeletal...
Tonikian, Raffi, Xin, Xiaofeng, Toret, Christopher P., Gfeller, David, Landgraf, Christiane, Panni, Simona, ...
A genome-scale specificity and interaction map for yeast SH3 domain-containing proteins reveal how family members show selective binding to target proteins and predicts the dynamic localization of...
Hausmann, Stéphane, Zheng, Sushuang, Costanzo, Michael, Brost, Renee L., Garcin, Dominique, Boone, Charles, ...
Trimethylguanosine synthase (Tgs1) is the enzyme that converts standard m7G caps to the 2,2,7-trimethylguanosine (TMG) caps characteristic of spliceosomal small nuclear RNAs. Fungi and mammalian...