Research Topics
Genomes and Genes | H D MadhaniSummaryAffiliation: University of California Country: USA Publications
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Publications
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatinMichael S Kobor
Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
PLoS Biol 2:E131. 2004..Metazoan orthologs of Swr1p (Drosophila Domino; human SRCAP and p400) may have analogous functions...- Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformansOliver W Liu
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158 2200, USA
Eukaryot Cell 6:630-40. 2007..Unlike acapsular strains, these mutant strains induced delayed symptoms of cryptococcosis, though the infected animals eventually contained the infection and recovered... - Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutantsH D Madhani
Whitehead Massachusetts Institute of Technology, Center for Genome Research, Department of Biology, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 96:12530-5. 1999..Thus, the Kss1 MAPK cascade programs development by coordinately modulating a cell adhesion factor, a secreted host-destroying activity, and a specialized subunit of the Cdc28 cyclin-dependent kinase... 
MAP kinases with distinct inhibitory functions impart signaling specificity during yeast differentiationH D Madhani
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Cell 91:673-84. 1997..In the absence of Fus3, there is erroneous crosstalk in which mating pheromone now activates filamentation-specific gene expression using the Kss1 MAPK...- Combinatorial control required for the specificity of yeast MAPK signalingH D Madhani
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 275:1314-7. 1997..An FRE in the TEC1 promoter functions in a positive feedback loop required for pseudohyphal development... - Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatinRyan M Raisner
Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, California 94143, USA
Cell 123:233-48. 2005..Efficient deposition of H2A.Z is further promoted by a specific pattern of histone H3 and H4 tail acetylation and the bromodomain protein Bdf1, a component of the Swr1 remodeling complex that deposits H2A.Z... - Principles of MAP kinase signaling specificity in Saccharomyces cerevisiaeMonica A Schwartz
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
Annu Rev Genet 38:725-48. 2004..Although much remains to be learned, current data indicate that scaffolding and cross pathway inhibition play key roles in the maintenance of fidelity... - Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperatureEric D Chow
Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158 2200, USA
Curr Genet 52:137-48. 2007..Resources described here should facilitate future investigations of this lethal human yeast pathogen... - Genomewide screen for negative regulators of sirtuin activity in Saccharomyces cerevisiae reveals 40 loci and links to metabolismRyan M Raisner
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158 2200, USA
Genetics 179:1933-44. 2008..We speculate that PAS kinase may integrate metabolic signals to control sirtuin activity... - Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformansOliver W Liu
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th St, GH N372C, San Francisco, CA 94158, USA
Cell 135:174-88. 2008..In particular, we describe a GATA family transcription factor that inhibits phagocytosis by murine macrophages independently of the capsule, indicating a previously unknown mechanism of innate immune modulation... - A link between virulence and homeostatic responses to hypoxia during infection by the human fungal pathogen Cryptococcus neoformansCheryl D Chun
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
PLoS Pathog 3:e22. 2007.... - Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificityTeresa R Shock
Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
Eukaryot Cell 8:606-16. 2009..Our results demonstrate that HOG signaling interrupts the FG pathway signal transduction between the phosphorylation of Kss1 and the activation of DNA binding by Tec1... - Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathwayEmma McCullagh
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA
Nat Cell Biol 12:954-62. 2010..Consequently, cells may have evolved mechanisms to suppress noise by controlling these interactions... - Pheromone-dependent destruction of the Tec1 transcription factor is required for MAP kinase signaling specificity in yeastMarie Z Bao
Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA 94143, USA
Cell 119:991-1000. 2004..Signal-induced destruction of a transcription factor for a competing pathway provides a mechanism for signaling specificity... - The control of filamentous differentiation and virulence in fungiH D Madhani
Whitehead Institute for Biomedical Research, Nine Cambridge Center, MA 02142, USA
Trends Cell Biol 8:348-53. 1998..Strikingly, components used to signal sexual differentiation in the response to mating pheromones are often reutilized to regulate dimorphic development, suggesting an ancient link between these processes... - The riddle of MAP kinase signaling specificityH D Madhani
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
Trends Genet 14:151-5. 1998..How are the myriad of inputs transduced accurately so that each evokes a specific response? One mechanism would be to have a distinct MAPK cascade for each signal; however, the situation appears to be more complicated... - Mechanisms that specify promoter nucleosome location and identityPaul D Hartley
Department of Biochemistry and Biophysics, University of California, San Francisco, 94158, USA
Cell 137:445-58. 2009..Z deposition using a steroid-inducible protein splicing strategy, we show that NFR establishment is necessary for H2A.Z deposition. These studies suggest an ordered pathway for the assembly of promoter chromatin architecture... - A comprehensive strategy enabling high-resolution functional analysis of the yeast genomeDavid K Breslow
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA
Nat Methods 5:711-8. 2008..Finally, by measuring the fitness of strains in the yeast deletion library, we addressed an enigma regarding the apparent prevalence of gene dispensability and found that most genes do contribute to growth... - Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.ZShivkumar Venkatasubrahmanyam
Department of Biochemistry and Biophysics, University of California, 600 16th Street, MC 2200, San Francisco, CA 94158, USA
Proc Natl Acad Sci U S A 104:16609-14. 2007..Antisilencing mechanisms may therefore cooperate to play a considerably broader role in regulating genome-wide transcription than previously thought... - Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatinMarc D Meneghini
Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
Cell 112:725-36. 2003..Thus, euchromatin and heterochromatin each contains components that antagonize switching to the opposite chromatin state... - Control of MAPK signaling specificity by a conserved residue in the MEK-binding domain of the yeast scaffold protein Ste5Monica A Schwartz
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th St, 94143-2200, USA
Curr Genet 49:351-63. 2006..These studies demonstrate a role for an endogenous scaffold in signaling specificity... - Nonredundant requirement for multiple histone modifications for the early anaphase release of the mitotic exit regulator Cdc14 from nucleolar chromatinWilliam W Hwang
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
PLoS Genet 5:e1000588. 2009..The nonredundant role for these modifications in this context contrasts with the notion of a highly combinatorial code by which histone marks act to control biological processes... - Multisite phosphorylation of the Saccharomyces cerevisiae filamentous growth regulator Tec1 is required for its recognition by the E3 ubiquitin ligase adaptor Cdc4 and its subsequent destruction in vivoMarie Z Bao
Department of Biochemistry and Biophysics, University of California, 600 16th St, MC2200, San Francisco, CA 94158 2200, USA
Eukaryot Cell 9:31-6. 2010.... - Selective kinase inhibition by exploiting differential pathway sensitivityCharles Kung
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, California 94143, USA
Chem Biol 13:399-407. 2006..Identification of highly sensitive kinases may provide a means to achieve selective perturbation of kinase signaling pathways complementary to efforts to achieve maximal differences between in vitro IC50 values... - A conserved RING finger protein required for histone H2B monoubiquitination and cell size controlWilliam W Hwang
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
Mol Cell 11:261-6. 2003..Notably, analysis of mutants demonstrates a function for Bre1/Lge1-dependent H2B monoubiquitination in the control of cell size... - Functional analysis of protein kinase networks in living cells: beyond "knock-outs" and "knock-downs"Hiten D Madhani
Department of Biochemistry and Biophysics, University of California, 600 16th St, San Fransico, CA 94143 2200, USA
Methods 40:251-4. 2006..The goal of this article is to provide a brief introductory primer into these issues using examples from yeast MAPK cascades and to motivate future systematic genetic analysis focusing on individual residues of protein kinases... - Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complexRachel Tompa
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
Genetics 175:585-93. 2007..Thus, antagonism of silencing is independent of the only known effector of this conserved histone modification... - Ers1, a rapidly diverging protein essential for RNA interference-dependent heterochromatic silencing in Schizosaccharomyces pombeMathieu Rougemaille
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
J Biol Chem 283:25770-3. 2008..Surprisingly, Ers1 lacks obvious orthologs outside of the genus Schizosaccharomyces. Within this group, it is diverging rapidly, raising the possibility that it is coevolving with target RNA elements... - Chemical genomic profiling to identify intracellular targets of a multiplex kinase inhibitorCharles Kung
Computational, Analytical, and Structural Sciences, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA
Proc Natl Acad Sci U S A 102:3587-92. 2005..Our results suggest that the cellular responses induced by multiplex protein kinase inhibitors may be an emergent property that cannot be understood fully by considering only the sum of individual inhibitor-kinase interactions...
Research Grants
- Epigenetic Regulation by Histone SubstitutionHiten Madhani; Fiscal Year: 2006..Indeed, chemical inhibitors of histone deacetylases, which are required for epigenetic gene silencing in all systems characterized from yeast to humans, are in clinical trials as anticancer drugs. ..