Genomes and Genes
Experts and Doctors on arabidopsis in New York, United States
Locale: New York, United States
Publications108 found, 100 shown here
- Tzfadia O, Amar D, Bradbury L, Wurtzel E, Shamir R. The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. Plant Cell. 2012;24:4389-406 pubmed publisher..MORPH candidates ranked for the carotenoid pathway from Arabidopsis and tomato are derived from pathways that compete for common precursors or from pathways that are coregulated with or regulate the carotenoid biosynthetic pathway. ..
- Lodha M, Marco C, Timmermans M. The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev. 2013;27:596-601 pubmed publisher..Combined with recent studies in mammals, our findings reveal a conserved paradigm to epigenetically regulate homeobox gene expression during development. ..
- Xu J, Chua N. Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation. EMBO J. 2012;31:1975-84 pubmed publisher..Our results suggest that mRNA decapping through MPK6-DCP1-DCP5 pathway serves as a rapid response to dehydration stress in Arabidopsis. ..
- Stamnes M, Craighead M, Hoe M, Lampen N, Geromanos S, Tempst P, et al. An integral membrane component of coatomer-coated transport vesicles defines a family of proteins involved in budding. Proc Natl Acad Sci U S A. 1995;92:8011-5 pubmed..Together, these results indicate a role for this protein family in the budding of coatamer-coated and other species of coated vesicles...
- Zhou Q, Hare P, Yang S, Zeidler M, Huang L, Chua N. FHL is required for full phytochrome A signaling and shares overlapping functions with FHY1. Plant J. 2005;43:356-70 pubmed..These findings reiterate the prevalence of partial degeneracy in plant signaling networks that regulate responses crucial to survival. ..
- Phelps Durr T, Thomas J, Vahab P, Timmermans M. Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell. 2005;17:2886-98 pubmed publisher..Components of this process are conserved in animals, suggesting the possibility that a similar epigenetic mechanism maintains determinacy during both plant and animal development...
- Sanchez J, Duque P, Chua N. ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant J. 2004;38:381-95 pubmed
- Heilmann I, Mekhedov S, King B, Browse J, Shanklin J. Identification of the Arabidopsis palmitoyl-monogalactosyldiacylglycerol delta7-desaturase gene FAD5, and effects of plastidial retargeting of Arabidopsis desaturases on the fad5 mutant phenotype. Plant Physiol. 2004;136:4237-45 pubmed..Tight correlation between leaf 16:3Delta(7,10,13) levels and chlorophyll content suggests a role for plastidial fatty acid desaturases in thylakoid formation. ..
- Tyszkiewicz A, Muir T. Activation of protein splicing with light in yeast. Nat Methods. 2008;5:303-5 pubmed publisher..Studies in Saccharomyces cerevisiae demonstrate that fusion of a photodimerization system from Arabidopsis thaliana to an artificially split intein permits rapid activation of protein splicing to yield a new protein product. ..
- Ueki S, Lacroix B, Krichevsky A, Lazarowitz S, Citovsky V. Functional transient genetic transformation of Arabidopsis leaves by biolistic bombardment. Nat Protoc. 2009;4:71-7 pubmed publisher..Using this procedure, the data are obtained after 2-4 d of work. ..
- Jang I, Chung P, Hemmes H, Jung C, Chua N. Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. Plant Cell. 2011;23:459-70 pubmed publisher..The presence of activating and repressive histone marks suggests a mechanism for the rapid and reversible regulation of phyA by dark and light. ..
- Jang I, Niu Q, Deng S, Zhao P, Chua N. Enhancing protein stability with retained biological function in transgenic plants. Plant J. 2012;72:345-54 pubmed publisher..1, which is involved in jasmonate signaling. Taken together, our results suggest that UBA fusions can be used to increase the stability of unstable proteins for basic plant biology research as well as crop improvement. ..
- Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, et al. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell. 2012;24:4333-45 pubmed publisher..RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of intron-containing lincRNAs. ..
- Lopez Molina L, Mongrand S, Chua N. A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in Arabidopsis. Proc Natl Acad Sci U S A. 2001;98:4782-7 pubmed..As expected for a key player in ABA-triggered processes, ABI5 protein accumulation, phosphorylation, stability, and activity are highly regulated by ABA during germination and early seedling growth. ..
- Møller S, Kim Y, Kunkel T, Chua N. PP7 is a positive regulator of blue light signaling in Arabidopsis. Plant Cell. 2003;15:1111-9 pubmed..Based on our findings and recent data regarding cryptochrome action, we propose that AtPP7 acts as a positive regulator of cryptochrome signaling in Arabidopsis. ..
- Niu Q, Lin S, Reyes J, Chen K, Wu H, Yeh S, et al. Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol. 2006;24:1420-8 pubmed..The amiRNA-mediated approach should have broad applicability for engineering multiple virus resistance in crop plants...
- Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma H. DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation. Plant Cell. 1996;8:81-94 pubmed..Finally, we show that several plant MADS domain proteins can bind to DNA either as homodimers or as heterodimers, suggesting that the number of different regulators could be much greater than the number of MADS box genes. ..
- Lemichez E, Wu Y, Sanchez J, Mettouchi A, Mathur J, Chua N. Inactivation of AtRac1 by abscisic acid is essential for stomatal closure. Genes Dev. 2001;15:1808-16 pubmed..Moreover, the dominant-negative form of AtRac1 could also restore stomatal closure in abi1-1. These results define AtRac1 as a central element for plant adaptation to drought. ..
- Lois L, Lima C, Chua N. Small ubiquitin-like modifier modulates abscisic acid signaling in Arabidopsis. Plant Cell. 2003;15:1347-59 pubmed..Reduction of AtSCE1a expression levels accentuates ABA-mediated growth inhibition. Our results suggest a role for SUMO in the modulation of the ABA signal transduction pathway. ..
- Catala R, Ouyang J, Abreu I, Hu Y, Seo H, Zhang X, et al. The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell. 2007;19:2952-66 pubmed..From these results, we conclude that SIZ1 regulates Arabidopsis growth and that this SUMO E3 ligase plays a role in drought stress response likely through the regulation of gene expression. ..
- Lonien J, Schwender J. Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis. Plant Physiol. 2009;151:1617-34 pubmed publisher..No such limited compensatory bypass could be observed in pkpbeta(1)pkpalpha. ..
- Bolle C, Koncz C, Chua N. PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Genes Dev. 2000;14:1269-78 pubmed..The results indicate that the truncated PAT1 protein acts in a dominant-negative fashion to inhibit phyA signaling. ..
- Zuo J, Niu Q, Nishizawa N, Wu Y, Kost B, Chua N. KORRIGAN, an Arabidopsis endo-1,4-beta-glucanase, localizes to the cell plate by polarized targeting and is essential for cytokinesis. Plant Cell. 2000;12:1137-52 pubmed..Our results suggest that KOR1 plays a critical role during cytokinesis. ..
- Nakajima K, Sena G, Nawy T, Benfey P. Intercellular movement of the putative transcription factor SHR in root patterning. Nature. 2001;413:307-11 pubmed..These results support a model in which SHR protein acts both as a signal from the stele and as an activator of endodermal cell fate and SCR-mediated cell division. ..
- Jang I, Yang S, Yang J, Chua N. Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling. Genes Dev. 2007;21:2100-11 pubmed
- Hemmes H, Henriques R, Jang I, Kim S, Chua N. Circadian clock regulates dynamic chromatin modifications associated with Arabidopsis CCA1/LHY and TOC1 transcriptional rhythms. Plant Cell Physiol. 2012;53:2016-29 pubmed publisher..Analysis of clock-compromised CCA1-overexpressing lines provided evidence that light/dark photoperiods signal the establishment of these chromatin changes which are gated by the clock. ..
- Lopez Molina L, Mongrand S, Kinoshita N, Chua N. AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation. Genes Dev. 2003;17:410-8 pubmed..Our results suggest that AFP attenuates ABA signals by targeting ABI5 for ubiquitin-mediated degradation in nuclear bodies. ..
- Ronemus M, Vaughn M, Martienssen R. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell. 2006;18:1559-74 pubmed..These results indicate that a subset of endogenous mRNA targets of RNA interference may be regulated through a mechanism of second-strand RNA synthesis and degradation initiated by or in addition to miRNA-mediated cleavage. ..
- Reyes J, Chua N. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J. 2007;49:592-606 pubmed..Our results suggest that ABA-induced accumulation of miR159 is a homeostatic mechanism to direct MYB33 and MYB101 transcript degradation to desensitize hormone signaling during seedling stress responses. ..
- Billon P, Bryant E, Joseph S, Nambiar T, Hayward S, Rothstein R, et al. CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons. Mol Cell. 2017;67:1068-1079.e4 pubmed publisher..Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP. ..
- Oliveira I, Brenner E, Chiu J, Hsieh M, Kouranov A, Lam H, et al. Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway. Braz J Med Biol Res. 2001;34:567-75 pubmed..Based on our observations on the biology of both structural and regulatory genes of the nitrogen assimilatory pathway, we have developed a model for metabolic control of the genes involved in the nitrogen assimilatory pathway in plants. ..
- Kiba T, Henriques R, Sakakibara H, Chua N. Targeted degradation of PSEUDO-RESPONSE REGULATOR5 by an SCFZTL complex regulates clock function and photomorphogenesis in Arabidopsis thaliana. Plant Cell. 2007;19:2516-30 pubmed..Together, our results show that ZTL targets PRR5 for degradation by 26S proteasomes in the circadian clock and in early photomorphogenesis. ..
- Gutierrez R, Stokes T, Thum K, Xu X, Obertello M, Katari M, et al. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A. 2008;105:4939-44 pubmed publisher..Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function. ..
- Borges F, Calarco J, Martienssen R. Reprogramming the epigenome in Arabidopsis pollen. Cold Spring Harb Symp Quant Biol. 2012;77:1-5 pubmed publisher..These results have led to a new model for the establishment and transgenerational maintenance of epigenetic marks in flowering plants. ..
- Seo H, Watanabe E, Tokutomi S, Nagatani A, Chua N. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev. 2004;18:617-22 pubmed..Our results indicate that COP1 acts as an E3 ligase to regulate phyA signaling by targeting elimination of the phyA photoreceptor itself. ..
- Yang G, Gao P, Zhang H, Huang S, Zheng Z. A mutation in MRH2 kinesin enhances the root hair tip growth defect caused by constitutively activated ROP2 small GTPase in Arabidopsis. PLoS ONE. 2007;2:e1074 pubmed
- Yang J, Iwasaki M, Machida C, Machida Y, Zhou X, Chua N. betaC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses. Genes Dev. 2008;22:2564-77 pubmed publisher..Our results show that betaC1 forms a complex with AS1 to execute its pathogenic functions and to suppress a subset of JA responses. ..
- Lam H, Coschigano K, Schultz C, Melo Oliveira R, Tjaden G, Oliveira I, et al. Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis. Plant Cell. 1995;7:887-98 pubmed
- Takahashi T, Mu J, Gasch A, Chua N. Identification by PCR of receptor-like protein kinases from Arabidopsis flowers. Plant Mol Biol. 1998;37:587-96 pubmed..Recombinant RKF1, produced in Escherichia coli, was found to have kinase activity with serine/threonine specificity in vitro. ..
- Klahre U, Chua N. The Arabidopsis actin-related protein 2 (AtARP2) promoter directs expression in xylem precursor cells and pollen. Plant Mol Biol. 1999;41:65-73 pubmed..In addition, strong expression was observed in pollen grains. We discuss the potential role of an arp2/3 complex in plant development. ..
- Helariutta Y, Fukaki H, Wysocka Diller J, Nakajima K, Jung J, Sena G, et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell. 2000;101:555-67 pubmed..Consistent with a regulatory role in radial patterning, ectopic expression of SHR results in supernumerary cell divisions and abnormal cell specification in the root meristem. ..
- Banno H, Chua N. Characterization of the arabidopsis formin-like protein AFH1 and its interacting protein. Plant Cell Physiol. 2000;41:617-26 pubmed..AFH1 may form a membrane anchored complex with FIP2, which might be involved in the organization of the actin cytoskeleton...
- Shevell D, Kunkel T, Chua N. Cell wall alterations in the arabidopsis emb30 mutant. Plant Cell. 2000;12:2047-60 pubmed..Together, these results suggest that emb30 mutations result in an abnormal cell wall, which in turn may account for the defects in cell adhesion and polar cell growth control observed in the mutants. ..
- Møller S, Kunkel T, Chua N. A plastidic ABC protein involved in intercompartmental communication of light signaling. Genes Dev. 2001;15:90-103 pubmed
- Sanchez J, Chua N. Arabidopsis PLC1 is required for secondary responses to abscisic acid signals. Plant Cell. 2001;13:1143-54 pubmed..We propose that AtPLC1 plays a role in secondary ABA responses. ..
- Ikeda Y, Banno H, Niu Q, Howell S, Chua N. The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls cotyledon development. Plant Cell Physiol. 2006;47:1443-56 pubmed..Phenotypes of induced ESR2 expression in a cuc1-1 mutant background were suppressed. Our results suggest that ESR2 plays a role in shoot regeneration through transcriptional regulation of CUC1. ..
- Xu J, Yang J, Niu Q, Chua N. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell. 2006;18:3386-98 pubmed..We conclude that mRNA turnover mediated by the decapping complex is required for postembryonic development in Arabidopsis. ..
- Chen H, Bandyopadhyay S, Shasha D, BIRNBAUM K. Predicting genome-wide redundancy using machine learning. BMC Evol Biol. 2010;10:357 pubmed publisher..The predictions and gene pair attributes for Arabidopsis provide a new resource for research in genetics and genome evolution. These techniques can now be applied to other organisms. ..
- Woo J, MacPherson C, Liu J, Wang H, Kiba T, Hannah M, et al. The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biol. 2012;12:62 pubmed publisher..The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation...
- Goulah C, Zhu G, Koszelak Rosenblum M, Malkowski M. The crystal structure of α-Dioxygenase provides insight into diversity in the cyclooxygenase-peroxidase superfamily. Biochemistry. 2013;52:1364-72 pubmed publisher..The α-DOX structure represents the first member of the α-DOX subfamily to be structurally characterized within the cyclooxygenase-peroxidase family of heme-containing proteins. ..
- Jang I, Henriques R, Chua N. Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A. Plant Cell Physiol. 2013;54:907-16 pubmed publisher..Together, our results suggest that HY5 transmits phyA signals through an FHY1/FHL-independent pathway but it may also modulate FHY1/FHL signal through its interaction with HFR1 and LAF1. ..
- Leu W, Cao X, Wilson T, Snustad D, Chua N. Phytochrome A and phytochrome B mediate the hypocotyl-specific downregulation of TUB1 by light in arabidopsis. Plant Cell. 1995;7:2187-96 pubmed..Histochemical analysis of transgenic plants expressing a TUB1-beta-glucuronidase chimeric transgene indicated that the downregulation observed only in hypocotyls and not in roots is controlled transcriptionally. ..
- Klahre U, Friederich E, Kost B, Louvard D, Chua N. Villin-like actin-binding proteins are expressed ubiquitously in Arabidopsis. Plant Physiol. 2000;122:35-48 pubmed..Green fluorescent protein fused to full-length AtVLN and individual AtVLN headpiece domains can bind to both animal and plant actin filaments in vivo. ..
- Hoth S, Morgante M, Sanchez J, Hanafey M, Tingey S, Chua N. Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J Cell Sci. 2002;115:4891-900 pubmed..However, a subset of genes continued to be appropriately regulated by ABA, which suggests the presence of at least two ABA signaling pathways, only one of which is blocked in abi1-1. ..
- Hare P, Moller S, Huang L, Chua N. LAF3, a novel factor required for normal phytochrome A signaling. Plant Physiol. 2003;133:1592-604 pubmed
- Xin Z, Wang A, Yang G, Gao P, Zheng Z. The Arabidopsis A4 subfamily of lectin receptor kinases negatively regulates abscisic acid response in seed germination. Plant Physiol. 2009;149:434-44 pubmed publisher..1 and LecRKA4.2 regulate some of the ABA-responsive genes. Taken together, our results demonstrate that the A4 subfamily of LecRKs has a redundant function in the negative regulation of ABA response in seed germination. ..
- Lee E, Cibrián Jaramillo A, Kolokotronis S, Katari M, Stamatakis A, Ott M, et al. A functional phylogenomic view of the seed plants. PLoS Genet. 2011;7:e1002411 pubmed publisher..Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification. ..
- Zalepa King L, Citovsky V. A plasmodesmal glycosyltransferase-like protein. PLoS ONE. 2013;8:e58025 pubmed publisher..Initial characterization of an Arabidopsis T-DNA insertional mutant in the AtGnTL gene revealed defects in seed germination and delayed plant growth. ..
- Lee J, Yi L, Li J, Schweitzer K, Borgmann M, Naumann M, et al. Crystal structure and versatile functional roles of the COP9 signalosome subunit 1. Proc Natl Acad Sci U S A. 2013;110:11845-50 pubmed publisher..Therefore, the CSN complex uses multiple mechanisms to hinder NF-?B activation, a principle likely to hold true for its regulation of many other targets and pathways...
- Oliveira I, Coruzzi G. Carbon and amino acids reciprocally modulate the expression of glutamine synthetase in Arabidopsis. Plant Physiol. 1999;121:301-10 pubmed..This type of GS gene regulation is reminiscent of the nitrogen regulatory system in bacteria, and suggests an evolutionary link between metabolic sensing and signaling in bacteria and plants. ..
- Banno H, Ikeda Y, Niu Q, Chua N. Overexpression of Arabidopsis ESR1 induces initiation of shoot regeneration. Plant Cell. 2001;13:2609-18 pubmed..Our results suggest that ESR1 may regulate the induction of shoot regeneration after the acquisition of competence for organogenesis. ..
- Zhang X, Yuan Y, Pei Y, Lin S, Tuschl T, Patel D, et al. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 2006;20:3255-68 pubmed..These findings provide insight on the molecular arms race between host antiviral RNA silencing and virus counterdefense...
- Bommert P, Nagasawa N, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet. 2013;45:334-7 pubmed publisher..These findings indicate that modulation of fundamental stem cell proliferation control pathways has the potential to enhance crop yields...
- Lam H, Peng S, Coruzzi G. Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana. Plant Physiol. 1994;106:1347-57 pubmed
- Hsieh M, Lam H, van de Loo F, Coruzzi G. A PII-like protein in Arabidopsis: putative role in nitrogen sensing. Proc Natl Acad Sci U S A. 1998;95:13965-70 pubmed
- Hausmann S, Koiwa H, Krishnamurthy S, Hampsey M, Shuman S. Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases. J Biol Chem. 2005;280:37681-8 pubmed..We surmise that the reading of the CTD code does not obey uniform rules with respect to the location and phasing of specificity determinants. Thus, CTD code, like the CTD structure, is plastic. ..
- Chen Y, Li F, Wurtzel E. Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiol. 2010;153:66-79 pubmed publisher..Therefore, plant carotenogenesis evolved by recruitment of genes from noncarotenogenic bacteria. ..
- Gou J, Felippes F, Liu C, Weigel D, Wang J. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011;23:1512-22 pubmed publisher..Our results reveal a direct link between the transition to flowering and secondary metabolism and provide a potential target for manipulation of anthocyanin and flavonol content in plants. ..
- Kinoshita N, Wang H, Kasahara H, Liu J, Macpherson C, Machida Y, et al. IAA-Ala Resistant3, an evolutionarily conserved target of miR167, mediates Arabidopsis root architecture changes during high osmotic stress. Plant Cell. 2012;24:3590-602 pubmed publisher..Sequence comparison revealed the miR167 target site on IAR3 mRNA is conserved in evolutionarily distant plant species. Finally, we showed that IAR3 is required for drought tolerance. ..
- Rosas U, Cibrián Jaramillo A, Ristova D, Banta J, Gifford M, Fan A, et al. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A. 2013;110:15133-8 pubmed publisher..This finding supports a role for plasticity responses in phenotypic evolution in natural environments. ..
- Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21:64-72 pubmed publisher..The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA. ..
- Foster R, Chua N. An Arabidopsis mutant with deregulated ABA gene expression: implications for negative regulator function. Plant J. 1999;17:363-72 pubmed..Genetic analyses indicate that the ade1 mutant is a monogenic recessive trait. A role for negative regulator function in ABA signalling is discussed. ..
- Wysocka Diller J, Helariutta Y, Fukaki H, Malamy J, Benfey P. Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot. Development. 2000;127:595-603 pubmed..Our data provides evidence that the same molecular mechanism regulates the radial patterning of ground tissue in both root and shoot during embryogenesis as well as postembryonically. ..
- Lancien M, Martin M, Hsieh M, Leustek T, Goodman H, Coruzzi G. Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J. 2002;29:347-58 pubmed..Herein, we discuss the significance of NADH-GOGAT in non-photorespiratory ammonium assimilation and in glutamate synthesis required for plant development. ..
- Duque P, Chua N. IMB1, a bromodomain protein induced during seed imbibition, regulates ABA- and phyA-mediated responses of germination in Arabidopsis. Plant J. 2003;35:787-99 pubmed..In imbibed seeds, IMB1 modulates the transcription of a battery of genes, providing clues on its mode of action. ..
- Zeidler M, Zhou Q, Sarda X, Yau C, Chua N. The nuclear localization signal and the C-terminal region of FHY1 are required for transmission of phytochrome A signals. Plant J. 2004;40:355-65 pubmed..Together with the results from global expression analysis, our findings point to an important role of FHY1 in phyA signaling through its nuclear translocation and induction of gene expression. ..
- Ishikawa M, Kiba T, Chua N. The Arabidopsis SPA1 gene is required for circadian clock function and photoperiodic flowering. Plant J. 2006;46:736-46 pubmed..Our results indicate that SPA1 not only negatively controls phyA-mediated signaling in seedlings, but also regulates circadian rhythms and flowering time in plants. ..
- Fang Y, Spector D. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol. 2007;17:818-23 pubmed..On the basis of these data, we propose that D-bodies are crucial for orchestrating pri-miRNA processing and/or storage/assembly of miRNA-processing complexes in the nuclei of plant cells. ..
- Lin S, Martin R, Mongrand S, Vandenabeele S, Chen K, Jang I, et al. RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1-induced programmed cell death in Arabidopsis. Plant J. 2008;56:550-61 pubmed publisher..Our results suggest that RING1 acts as a signal from the plasma membrane lipid rafts to trigger the FB1-induced plant programmed cell death pathway. ..
- Erlich Y, Chang K, Gordon A, Ronen R, Navon O, Rooks M, et al. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res. 2009;19:1243-53 pubmed publisher..We achieved greater than 97% accuracy in these trials. The strategies reported here can be applied to a wide variety of biological problems, including the determination of genotypic variation within large populations of individuals. ..
- Hiratsuka K, Wu X, Fukuzawa H, Chua N. Molecular dissection of GT-1 from Arabidopsis. Plant Cell. 1994;6:1805-13 pubmed..Transient expression of the GT-1::beta-glucuronidase fusion protein in onion cells revealed the presence of a nuclear localization signal(s) within the first 215 amino acids of GT-1. ..
- Coschigano K, Melo Oliveira R, Lim J, Coruzzi G. Arabidopsis gls mutants and distinct Fd-GOGAT genes. Implications for photorespiration and primary nitrogen assimilation. Plant Cell. 1998;10:741-52 pubmed
- Roudier F, Schindelman G, DeSalle R, Benfey P. The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion. Plant Physiol. 2002;130:538-48 pubmed..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface. ..
- Kidner C, Martienssen R. The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol. 2005;280:504-17 pubmed..CLF is over expressed in ago1, showing that the RNAi pathway regulates polycomb-type epigenetic modifiers. ..