@article{11092, abstract = {To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function.}, author = {Savas, Jeffrey N. and Toyama, Brandon H. and Xu, Tao and Yates, John R. and HETZER, Martin W}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6071}, pages = {942--942}, publisher = {American Association for the Advancement of Science}, title = {{Extremely long-lived nuclear pore proteins in the rat brain}}, doi = {10.1126/science.1217421}, volume = {335}, year = {2012}, } @article{12198, abstract = {The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.}, author = {Ibarra, Christian A. and Feng, Xiaoqi and Schoft, Vera K. and Hsieh, Tzung-Fu and Uzawa, Rie and Rodrigues, Jessica A. and Zemach, Assaf and Chumak, Nina and Machlicova, Adriana and Nishimura, Toshiro and Rojas, Denisse and Fischer, Robert L. and Tamaru, Hisashi and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6100}, pages = {1360--1364}, publisher = {American Association for the Advancement of Science}, title = {{Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes}}, doi = {10.1126/science.1224839}, volume = {337}, year = {2012}, } @article{14305, abstract = {Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.}, author = {Bachmann, Annett and Wildemann, Dirk and Praetorius, Florian M and Fischer, Gunter and Kiefhaber, Thomas}, issn = {1091-6490}, journal = {PNAS}, keywords = {Multidisciplinary}, number = {10}, pages = {3952--3957}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction}}, doi = {10.1073/pnas.1012668108}, volume = {108}, year = {2011}, } @article{9452, abstract = {Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.}, author = {Zemach, Assaf and McDaniel, Ivy E. and Silva, Pedro and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5980}, pages = {916--919}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide evolutionary analysis of eukaryotic DNA methylation}}, doi = {10.1126/science.1186366}, volume = {328}, year = {2010}, } @article{13418, abstract = {In traditional photoconductors1,2,3, the impinging light generates mobile charge carriers in the valence and/or conduction bands, causing the material’s conductivity to increase4. Such positive photoconductance is observed in both bulk and nanostructured5,6 photoconductors. Here we describe a class of nanoparticle-based materials whose conductivity can either increase or decrease on irradiation with visible light of wavelengths close to the particles’ surface plasmon resonance. The remarkable feature of these plasmonic materials is that the sign of the conductivity change and the nature of the electron transport between the nanoparticles depend on the molecules comprising the self-assembled monolayers (SAMs)7,8 stabilizing the nanoparticles. For SAMs made of electrically neutral (polar and non-polar) molecules, conductivity increases on irradiation. If, however, the SAMs contain electrically charged (either negatively or positively) groups, conductivity decreases. The optical and electrical characteristics of these previously undescribed inverse photoconductors can be engineered flexibly by adjusting the material properties of the nanoparticles and of the coating SAMs. In particular, in films comprising mixtures of different nanoparticles or nanoparticles coated with mixed SAMs, the overall photoconductance is a weighted average of the changes induced by the individual components. These and other observations can be rationalized in terms of light-induced creation of mobile charge carriers whose transport through the charged SAMs is inhibited by carrier trapping in transient polaron-like states9,10. The nanoparticle-based photoconductors we describe could have uses in chemical sensors and/or in conjunction with flexible substrates.}, author = {Nakanishi, Hideyuki and Bishop, Kyle J. M. and Kowalczyk, Bartlomiej and Nitzan, Abraham and Weiss, Emily A. and Tretiakov, Konstantin V. and Apodaca, Mario M. and Klajn, Rafal and Stoddart, J. Fraser and Grzybowski, Bartosz A.}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7253}, pages = {371--375}, publisher = {Springer Nature}, title = {{Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles}}, doi = {10.1038/nature08131}, volume = {460}, year = {2009}, } @article{9453, abstract = {Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.}, author = {Hsieh, Tzung-Fu and Ibarra, Christian A. and Silva, Pedro and Zemach, Assaf and Eshed-Williams, Leor and Fischer, Robert L. and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5933}, pages = {1451--1454}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide demethylation of Arabidopsis endosperm}}, doi = {10.1126/science.1172417}, volume = {324}, year = {2009}, } @article{11114, abstract = {We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment.}, author = {Schulte, Roberta and Talamas, Jessica and Doucet, Christine and HETZER, Martin W}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions}}, doi = {10.1371/journal.pone.0002061}, volume = {3}, year = {2008}, } @article{9457, abstract = {Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.}, author = {Zilberman, Daniel and Coleman-Derr, Devin and Ballinger, Tracy and Henikoff, Steven}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7218}, pages = {125--129}, publisher = {Springer Nature}, title = {{Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks}}, doi = {10.1038/nature07324}, volume = {456}, year = {2008}, } @article{8483, abstract = {Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.}, author = {Schanda, Paul and Forge, V. and Brutscher, B.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {27}, pages = {11257--11262}, publisher = {National Academy of Sciences}, title = {{Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy}}, doi = {10.1073/pnas.0702069104}, volume = {104}, year = {2007}, } @article{13425, abstract = {Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates.}, author = {Klajn, Rafal and Bishop, Kyle J. M. and Grzybowski, Bartosz A.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {25}, pages = {10305--10309}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures}}, doi = {10.1073/pnas.0611371104}, volume = {104}, year = {2007}, } @article{13427, abstract = {Deformable, spherical aggregates of metal nanoparticles connected by long-chain dithiol ligands self-assemble into nanostructured materials of macroscopic dimensions. These materials are plastic and moldable against arbitrarily shaped masters and can be thermally hardened into polycrystalline metal structures of controllable porosity. In addition, in both plastic and hardened states, the assemblies are electrically conductive and exhibit Ohmic characteristics down to ∼20 volts per meter. The self-assembly method leading to such materials is applicable both to pure metals and to bimetallic structures of various elemental compositions.}, author = {Klajn, Rafal and Bishop, Kyle J. M. and Fialkowski, Marcin and Paszewski, Maciej and Campbell, Christopher J. and Gray, Timothy P. and Grzybowski, Bartosz A.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5822}, pages = {261--264}, publisher = {American Association for the Advancement of Science}, title = {{Plastic and moldable metals by self-assembly of sticky nanoparticle aggregates}}, doi = {10.1126/science.1139131}, volume = {316}, year = {2007}, } @article{11118, abstract = {Nuclear pore complexes are multiprotein channels that span the double lipid bilayer of the nuclear envelope. How new pores are inserted into the intact nuclear envelope of proliferating and differentiating eukaryotic cells is unknown. We found that the Nup107-160 complex was incorporated into assembly sites in the nuclear envelope from both the nucleoplasmic and the cytoplasmic sides. Nuclear pore insertion required the generation of Ran guanosine triphosphate in the nuclear and cytoplasmic compartments. Newly formed nuclear pore complexes did not contain structural components of preexisting pores, suggesting that they can form de novo.}, author = {D'Angelo, Maximiliano A. and Anderson, Daniel J. and Richard, Erin and HETZER, Martin W}, issn = {0036-8075}, journal = {Science}, keywords = {Multidisciplinary}, number = {5772}, pages = {440--443}, publisher = {American Association for the Advancement of Science}, title = {{Nuclear pores form de novo from both sides of the nuclear envelope}}, doi = {10.1126/science.1124196}, volume = {312}, year = {2006}, } @article{9454, author = {Chan, Simon W.-L. and Zilberman, Daniel and Xie, Zhixin and Johansen, Lisa K. and Carrington, James C. and Jacobsen, Steven E.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5662}, pages = {1336}, publisher = {American Association for the Advancement of Science}, title = {{RNA silencing genes control de novo DNA methylation}}, doi = {10.1126/science.1095989}, volume = {303}, year = {2004}, } @article{11121, abstract = {In metazoa, the nuclear envelope breaks down and reforms during each cell cycle. Nuclear pore complexes (NPCs), which serve as channels for transport between the nucleus and cytoplasm1, assemble into the reforming nuclear envelope in a sequential process involving association of a subset of NPC proteins, nucleoporins, with chromatin followed by the formation of a closed nuclear envelope fenestrated by NPCs2,3,4,5,6,7. How chromatin recruitment of nucleoporins and NPC assembly are regulated is unknown. Here we demonstrate that RanGTP production is required to dissociate nucleoporins Nup107, Nup153 and Nup358 from Importin β, to target them to chromatin and to induce association between separate NPC subcomplexes. Additionally, either an excess of RanGTP or removal of Importin β induces formation of NPC-containing membrane structures—annulate lamellae—both in vitro in the absence of chromatin and in vivo. Annulate lamellae formation is strongly and specifically inhibited by an excess of Importin β. The data demonstrate that RanGTP triggers distinct steps of NPC assembly, and suggest a mechanism for the spatial restriction of NPC assembly to the surface of chromatin.}, author = {Walther, Tobias C. and Askjaer, Peter and Gentzel, Marc and Habermann, Anja and Griffiths, Gareth and Wilm, Matthias and Mattaj, Iain W. and HETZER, Martin W}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {6949}, pages = {689--694}, publisher = {Springer Nature}, title = {{RanGTP mediates nuclear pore complex assembly}}, doi = {10.1038/nature01898}, volume = {424}, year = {2003}, } @article{9455, abstract = {Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation.}, author = {Zilberman, Daniel and Cao, Xiaofeng and Jacobsen, Steven E.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5607}, pages = {716--719}, publisher = {American Association for the Advancement of Science}, title = {{ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation}}, doi = {10.1126/science.1079695}, volume = {299}, year = {2003}, } @article{9444, abstract = {Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.}, author = {Lindroth, A. M. and Cao, Xiaofeng and Jackson, James P. and Zilberman, Daniel and McCallum, Claire M. and Henikoff, Steven and Jacobsen, Steven E.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5524}, pages = {2077--2080}, publisher = {American Association for the Advancement of Science}, title = {{Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation}}, doi = {10.1126/science.1059745}, volume = {292}, year = {2001}, }