A genome-wide deletion mutant screen identifies pathways affected by nickel sulfate in Saccharomyces cerevisiae.

PubWeight™: 0.81‹?›

🔗 View Article (PMC 2784802)

Published in BMC Genomics on November 15, 2009

Authors

Adriana Arita1, Xue Zhou, Thomas P Ellen, Xin Liu, Jingxiang Bai, John P Rooney, Adrienne Kurtz, Catherine B Klein, Wei Dai, Thomas J Begley, Max Costa

Author Affiliations

1: New York University School of Medicine, Nelson Institute of Environmental Medicine, NY 10987, USA. aga240@nyumc.org

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76

Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52

Life with 6000 genes. Science (1996) 41.51

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25

ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science (2007) 20.11

Ubiquitin-dependent sorting into the multivesicular body pathway requires the function of a conserved endosomal protein sorting complex, ESCRT-I. Cell (2001) 9.08

FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics (2002) 8.01

Mechanism and regulation of mRNA polyadenylation. Genes Dev (1997) 7.48

TREX is a conserved complex coupling transcription with messenger RNA export. Nature (2002) 6.53

Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res (2002) 5.42

Endosome-associated complex, ESCRT-II, recruits transport machinery for protein sorting at the multivesicular body. Dev Cell (2002) 4.94

Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell (2005) 4.00

Genes required for ionizing radiation resistance in yeast. Nat Genet (2001) 3.43

Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol (2002) 3.18

A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J (2000) 3.11

CENP-F is a protein of the nuclear matrix that assembles onto kinetochores at late G2 and is rapidly degraded after mitosis. J Cell Biol (1995) 3.03

Cancers of the lung and nasal sinuses in nickel workers. Br J Cancer (1970) 2.67

Endosomal and non-endosomal functions of ESCRT proteins. Trends Cell Biol (2006) 2.61

Genetic and epigenetic mechanisms in metal carcinogenesis and cocarcinogenesis: nickel, arsenic, and chromium. Chem Res Toxicol (2007) 2.59

Structural and mechanistic studies of VPS4 proteins. EMBO J (2005) 2.58

A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proc Natl Acad Sci U S A (2001) 2.49

Identification of protein p270/Tpr as a constitutive component of the nuclear pore complex-attached intranuclear filaments. J Cell Biol (1997) 2.32

The transcription factor Rim101p governs ion tolerance and cell differentiation by direct repression of the regulatory genes NRG1 and SMP1 in Saccharomyces cerevisiae. Mol Cell Biol (2003) 2.29

Structural basis for endosomal targeting by the Bro1 domain. Dev Cell (2005) 2.28

Snf1 protein kinase and the repressors Nrg1 and Nrg2 regulate FLO11, haploid invasive growth, and diploid pseudohyphal differentiation. Mol Cell Biol (2002) 2.20

Carcinogenic nickel silences gene expression by chromatin condensation and DNA methylation: a new model for epigenetic carcinogens. Mol Cell Biol (1995) 2.14

Bro1 coordinates deubiquitination in the multivesicular body pathway by recruiting Doa4 to endosomes. J Cell Biol (2004) 1.93

Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2004) 1.90

Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol (2004) 1.90

Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell (2004) 1.81

Nickel ions increase histone H3 lysine 9 dimethylation and induce transgene silencing. Mol Cell Biol (2006) 1.77

Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol Cell Biol (2004) 1.76

Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol (2005) 1.70

Molecular evidence that the eukaryotic THO/TREX complex is required for efficient transcription elongation. J Biol Chem (2003) 1.63

Nrg1 is a transcriptional repressor for glucose repression of STA1 gene expression in Saccharomyces cerevisiae. Mol Cell Biol (1999) 1.63

Network of general and specialty J protein chaperones of the yeast cytosol. Proc Natl Acad Sci U S A (2007) 1.61

Genome-wide identification of genes conferring resistance to the anticancer agents cisplatin, oxaliplatin, and mitomycin C. Cancer Res (2004) 1.49

Human CHMP6, a myristoylated ESCRT-III protein, interacts directly with an ESCRT-II component EAP20 and regulates endosomal cargo sorting. Biochem J (2005) 1.48

Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature (2005) 1.41

Interference by toxic metal ions with DNA repair processes and cell cycle control: molecular mechanisms. Environ Health Perspect (2002) 1.37

Far3 and five interacting proteins prevent premature recovery from pheromone arrest in the budding yeast Saccharomyces cerevisiae. Mol Cell Biol (2003) 1.36

Senescence of nickel-transformed cells by an X chromosome: possible epigenetic control. Science (1991) 1.35

Use of a genome-wide approach to identify new genes that control resistance of Saccharomyces cerevisiae to ionizing radiation. Radiat Res (2003) 1.33

Alterations of histone modifications and transgene silencing by nickel chloride. Carcinogenesis (2006) 1.32

DNA methylation, heterochromatin and epigenetic carcinogens. Mutat Res (1997) 1.25

Global transcriptome and deletome profiles of yeast exposed to transition metals. PLoS Genet (2008) 1.23

Nickel carcinogenesis: epigenetics and hypoxia signaling. Mutat Res (2005) 1.19

NRG1 is required for glucose repression of the SUC2 and GAL genes of Saccharomyces cerevisiae. BMC Genet (2001) 1.17

Soluble nickel inhibits HIF-prolyl-hydroxylases creating persistent hypoxic signaling in A549 cells. Mol Carcinog (2006) 1.17

Nickel compounds induce phosphorylation of histone H3 at serine 10 by activating JNK-MAPK pathway. Carcinogenesis (2008) 1.14

Neoplastic transformation of human osteoblast cells to the tumorigenic phenotype by heavy metal-tungsten alloy particles: induction of genotoxic effects. Carcinogenesis (2001) 1.09

Mdt1, a novel Rad53 FHA1 domain-interacting protein, modulates DNA damage tolerance and G(2)/M cell cycle progression in Saccharomyces cerevisiae. Mol Cell Biol (2004) 1.08

Genetic basis of arsenite and cadmium tolerance in Saccharomyces cerevisiae. BMC Genomics (2009) 1.07

Nickel decreases cellular iron level and converts cytosolic aconitase to iron-regulatory protein 1 in A549 cells. Toxicol Appl Pharmacol (2004) 1.07

Carcinogenic effect of nickel compounds. Mol Cell Biochem (2005) 1.07

Nickel compounds are novel inhibitors of histone H4 acetylation. Cancer Res (2000) 1.06

Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast. Genome Biol (2008) 1.00

Inhibition of core histones acetylation by carcinogenic nickel(II). Mol Cell Biochem (2005) 0.98

Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics (2008) 0.95

Yeast genes involved in cadmium tolerance: Identification of DNA replication as a target of cadmium toxicity. DNA Repair (Amst) (2008) 0.93

Soluble and insoluble nickel compounds exert a differential inhibitory effect on cell growth through IKKalpha-dependent cyclin D1 down-regulation. J Cell Physiol (2009) 0.92

Proton gradient-driven nickel uptake by vacuolar membrane vesicles of Saccharomyces cerevisiae. J Bacteriol (1998) 0.92

Heterochromatinization as a potential mechanism of nickel-induced carcinogenesis. Biochemistry (2009) 0.91

The subcellular distribution of nickel in Ni-sensitive and Ni-resistant strains of Saccharomyces cerevisiae. Microbios (1992) 0.90

Identification and purification of the Holo-ELL complex. Evidence for the presence of ELL-associated proteins that suppress the transcriptional inhibitory activity of ELL. J Biol Chem (1998) 0.89

Genome-wide screening for genes whose deletions confer sensitivity to mutagenic purine base analogs in yeast. BMC Genet (2005) 0.87

Use of the Syrian hamster embryo cell transformation assay for determining the carcinogenic potential of heavy metal compounds. Fundam Appl Toxicol (1996) 0.85

Carcinogenic response of the nasal cavity to inhaled chemical mixtures. Mutat Res (1997) 0.85

Ni(II) affects ubiquitination of core histones H2B and H2A. Exp Cell Res (2006) 0.84

Microarray analysis of altered gene expression in murine fibroblasts transformed by nickel(II) to nickel(II)-resistant malignant phenotype. Toxicol Appl Pharmacol (2005) 0.83

The yeast genome: on the road to the Golden Age. Curr Opin Genet Dev (2000) 0.81

Molecular biology of nickel carcinogenesis: identification of differentially expressed genes in morphologically transformed C3H10T1/2 Cl 8 mouse embryo fibroblast cell lines induced by specific insoluble nickel compounds. Mol Cell Biochem (2004) 0.80

The molecular chaperones HSP28, GRP78, endoplasmin, and calnexin exhibit strikingly different levels in quiescent keratinocytes as compared to their proliferating normal and transformed counterparts: cDNA cloning and expression of calnexin. Electrophoresis (1994) 0.76

Articles by these authors

Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08

Prostate-specific deletion of the murine Pten tumor suppressor gene leads to metastatic prostate cancer. Cancer Cell (2003) 8.11

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20

Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

Hypoxia-inducible factor-1 (HIF-1). Mol Pharmacol (2006) 4.71

Cre/loxP-mediated inactivation of the murine Pten tumor suppressor gene. Genesis (2002) 4.23

Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74

A systems approach to mapping DNA damage response pathways. Science (2006) 3.55

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res (2011) 3.05

Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell (2007) 2.94

PTEN negatively regulates neural stem cell self-renewal by modulating G0-G1 cell cycle entry. Proc Natl Acad Sci U S A (2005) 2.93

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82

A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet (2010) 2.73

Apatinib for chemotherapy-refractory advanced metastatic gastric cancer: results from a randomized, placebo-controlled, parallel-arm, phase II trial. J Clin Oncol (2013) 2.69

The PSA(-/lo) prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration. Cell Stem Cell (2012) 2.69

Genetic characterization of Nipah virus, Bangladesh, 2004. Emerg Infect Dis (2005) 2.62

Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci U S A (2008) 2.60

Adaptive evolution of UGT2B17 copy-number variation. Am J Hum Genet (2008) 2.58

Rig-I-/- mice develop colitis associated with downregulation of G alpha i2. Cell Res (2007) 2.49

Principal axis-based correspondence between multiple cameras for people tracking. IEEE Trans Pattern Anal Mach Intell (2006) 2.47

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45

Conditional loss of PTEN leads to precocious development and neoplasia in the mammary gland. Development (2002) 2.42

T-cell and natural killer-cell large granular lymphocyte leukemia neoplasias. Leuk Lymphoma (2011) 2.37

Multiple genes for essential-hypertension susceptibility on chromosome 1q. Am J Hum Genet (2006) 2.34

BUBR1 deficiency results in abnormal megakaryopoiesis. Blood (2003) 2.31

NKX3.1 stabilizes p53, inhibits AKT activation, and blocks prostate cancer initiation caused by PTEN loss. Cancer Cell (2006) 2.29

Toxicity and carcinogenicity of chromium compounds in humans. Crit Rev Toxicol (2006) 2.24

Colonic tumorigenesis in BubR1+/-ApcMin/+ compound mutant mice is linked to premature separation of sister chromatids and enhanced genomic instability. Proc Natl Acad Sci U S A (2005) 2.15

sSgo1, a major splice variant of Sgo1, functions in centriole cohesion where it is regulated by Plk1. Dev Cell (2008) 2.12

PTEN dosage is essential for neurofibroma development and malignant transformation. Proc Natl Acad Sci U S A (2009) 2.07

Ulinastatin is a novel candidate drug for sepsis and secondary acute lung injury, evidence from an optimized CLP rat model. Int Immunopharmacol (2013) 2.06

Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J Biol Chem (2004) 2.06

A critical role of erythropoietin receptor in neurogenesis and post-stroke recovery. J Neurosci (2006) 2.04

Variability of antibiotic concentrations in critically ill patients receiving continuous renal replacement therapy: a multicentre pharmacokinetic study. Crit Care Med (2012) 2.04

Epigenetics in metal carcinogenesis: nickel, arsenic, chromium and cadmium. Metallomics (2009) 1.96

Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res (2011) 1.94

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun (2012) 1.93

Elevated phosphatidylinositol 3,4,5-trisphosphate in glia triggers cell-autonomous membrane wrapping and myelination. J Neurosci (2010) 1.93

Purple acid phosphatases of Arabidopsis thaliana. Comparative analysis and differential regulation by phosphate deprivation. J Biol Chem (2002) 1.93

Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2004) 1.90

A mutation in a novel ATP-dependent Lon protease gene in a kindred with mild mental retardation. Neurology (2004) 1.90

Cytochrome P450 2E1 contributes to ethanol-induced fatty liver in mice. Hepatology (2008) 1.90

Ultrasound-mediated tumor imaging and nanotherapy using drug loaded, block copolymer stabilized perfluorocarbon nanoemulsions. J Control Release (2011) 1.89

Deletion of the neuron-specific protein delta-catenin leads to severe cognitive and synaptic dysfunction. Curr Biol (2004) 1.80

Pten deletion in adult neural stem/progenitor cells enhances constitutive neurogenesis. J Neurosci (2009) 1.80

Hypoxic stress induces dimethylated histone H3 lysine 9 through histone methyltransferase G9a in mammalian cells. Cancer Res (2006) 1.78

Nickel ions increase histone H3 lysine 9 dimethylation and induce transgene silencing. Mol Cell Biol (2006) 1.77

Maternal embryonic leucine zipper kinase (MELK) regulates multipotent neural progenitor proliferation. J Cell Biol (2005) 1.74

Comparisons of image quality and radiation dose between iterative reconstruction and filtered back projection reconstruction algorithms in 256-MDCT coronary angiography. AJR Am J Roentgenol (2012) 1.73

3D noncontrast MR angiography of the distal lower extremities using flow-sensitive dephasing (FSD)-prepared balanced SSFP. Magn Reson Med (2009) 1.72

8q24 and prostate cancer: association with advanced disease and meta-analysis. Eur J Hum Genet (2008) 1.72

Haploinsufficiency of SGO1 results in deregulated centrosome dynamics, enhanced chromosomal instability and colon tumorigenesis. Cell Cycle (2012) 1.71

Ovarian cancer stem cell-like side populations are enriched following chemotherapy and overexpress EZH2. Mol Cancer Ther (2011) 1.70

L-fucose utilization provides Campylobacter jejuni with a competitive advantage. Proc Natl Acad Sci U S A (2011) 1.68

Molecular mechanisms of arsenic carcinogenesis. Mol Cell Biochem (2004) 1.66

GJB2 mutation spectrum in 2,063 Chinese patients with nonsyndromic hearing impairment. J Transl Med (2009) 1.66

Radiation dose reduction in computed tomography: techniques and future perspective. Imaging Med (2009) 1.65

Genetic background controls tumor development in PTEN-deficient mice. Cancer Res (2006) 1.63

Telbivudine or lamivudine use in late pregnancy safely reduces perinatal transmission of hepatitis B virus in real-life practice. Hepatology (2014) 1.62

Defects in chromosome congression and mitotic progression in KIF18A-deficient cells are partly mediated through impaired functions of CENP-E. Cell Cycle (2009) 1.62

Contrast-enhanced whole-heart coronary magnetic resonance angiography at 3.0-T: a comparative study with X-ray angiography in a single center. J Am Coll Cardiol (2009) 1.61

Cytometry of ATM activation and histone H2AX phosphorylation to estimate extent of DNA damage induced by exogenous agents. Cytometry A (2007) 1.59

Electromagnetic imaging methods for nondestructive evaluation applications. Sensors (Basel) (2011) 1.59

SUMO1 modification of PTEN regulates tumorigenesis by controlling its association with the plasma membrane. Nat Commun (2012) 1.58

Activation of ATM and histone H2AX phosphorylation induced by mitoxantrone but not by topotecan is prevented by the antioxidant N-acetyl-L-cysteine. Cancer Biol Ther (2006) 1.57

Essential role of AKT-1/protein kinase B alpha in PTEN-controlled tumorigenesis. Mol Cell Biol (2002) 1.57

Arsenic trioxide arrests cells early in mitosis leading to apoptosis. Cell Cycle (2002) 1.54

Development of two avidity-based assays to detect recent HIV type 1 seroconversion using a multisubtype gp41 recombinant protein. AIDS Res Hum Retroviruses (2010) 1.53

Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol (2010) 1.53

Discovery of marinopyrrole A (maritoclax) as a selective Mcl-1 antagonist that overcomes ABT-737 resistance by binding to and targeting Mcl-1 for proteasomal degradation. J Biol Chem (2012) 1.53

Arsenite alters global histone H3 methylation. Carcinogenesis (2008) 1.53

Architecture of an RNA polymerase II transcription pre-initiation complex. Science (2013) 1.52

Generation of a monkey with MECP2 mutations by TALEN-based gene targeting. Neurosci Bull (2014) 1.52

Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol (2011) 1.51

The regulation of hypoxic genes by calcium involves c-Jun/AP-1, which cooperates with hypoxia-inducible factor 1 in response to hypoxia. Mol Cell Biol (2002) 1.48

Genome-wide responses to DNA-damaging agents. Annu Rev Microbiol (2005) 1.48

Percent fat mass is inversely associated with bone mass and hip geometry in rural Chinese adolescents. J Bone Miner Res (2010) 1.47

Histone H2AX phosphorylation after cell irradiation with UV-B: relationship to cell cycle phase and induction of apoptosis. Cell Cycle (2005) 1.47

Epigenetics and the environment. Ann N Y Acad Sci (2003) 1.47

NDRG1, a growth and cancer related gene: regulation of gene expression and function in normal and disease states. Carcinogenesis (2007) 1.47

Podocalyxin variants and risk of prostate cancer and tumor aggressiveness. Hum Mol Genet (2006) 1.46

Application of ICHD-II criteria in a headache clinic of China. PLoS One (2012) 1.46

An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. Nat Commun (2011) 1.45

Molecular profiling of LGL leukemia reveals role of sphingolipid signaling in survival of cytotoxic lymphocytes. Blood (2008) 1.45

Cell cycle arrest and apoptosis induced by human Polo-like kinase 3 is mediated through perturbation of microtubule integrity. Mol Cell Biol (2002) 1.44

Identification of natural coumarin compounds that rescue defective DeltaF508-CFTR chloride channel gating. Clin Exp Pharmacol Physiol (2008) 1.43

A mechanism-based inactivator for histone demethylase LSD1. J Am Chem Soc (2006) 1.43

[Ln2(C2O4)2(pyzc)2(H2O)2]n[Ln = Pr (1), Er (2)]: novel two-dimensional lanthanide coordination polymers with 2-pyrazinecarboxylate and oxalate. Inorg Chem (2006) 1.41

Assembly information services in the European Nucleotide Archive. Nucleic Acids Res (2013) 1.40

Arsenic, mode of action at biologically plausible low doses: what are the implications for low dose cancer risk? Toxicol Appl Pharmacol (2005) 1.39

Regulation of cell cycle checkpoints by polo-like kinases. Oncogene (2005) 1.39

A cascade of protein kinase C isozymes promotes cytoskeletal polarization in T cells. Nat Immunol (2011) 1.39

Enhanced genomic instabilities caused by deregulated microtubule dynamics and chromosome segregation: a perspective from genetic studies in mice. Carcinogenesis (2009) 1.38

c-MYC-regulated miR-23a/24-2/27a cluster promotes mammary carcinoma cell invasion and hepatic metastasis by targeting Sprouty2. J Biol Chem (2013) 1.37

Laminar and compartmental regulation of dendritic growth in mature cortex. Nat Neurosci (2009) 1.37