@article{508,
  abstract     = {The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.},
  author       = {Tarazona Santos, Eduardo and Machado, Moara and Magalhães, Wagner and Chen, Renee and Lyon, Fernanda and Burdett, Laurie and Crenshaw, Andrew and Fabbri, Cristina and Pereira, Latife and Pinto, Laelia and Fernandes Redondo, Rodrigo A and Sestanovich, Ben and Yeager, Meredith and Chanock, Stephen},
  journal      = {Molecular Biology and Evolution},
  number       = {9},
  pages        = {2157 -- 2167},
  publisher    = {Oxford University Press},
  title        = {{Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications}},
  doi          = {10.1093/molbev/mst119},
  volume       = {30},
  year         = {2013},
}

@article{509,
  abstract     = {Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. },
  author       = {Di Rubbo, Simone and Irani, Niloufer and Kim, Soo and Xu, Zheng and Gadeyne, Astrid and Dejonghe, Wim and Vanhoutte, Isabelle and Persiau, Geert and Eeckhout, Dominique and Simon, Sibu and Song, Kyungyoung and Kleine Vehn, Jürgen and Friml, Jirí and De Jaeger, Geert and Van Damme, Daniël and Hwang, Inhwan and Russinova, Eugenia},
  journal      = {Plant Cell},
  number       = {8},
  pages        = {2986 -- 2997},
  publisher    = {American Society of Plant Biologists},
  title        = {{The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis}},
  doi          = {10.1105/tpc.113.114058},
  volume       = {25},
  year         = {2013},
}

@article{511,
  abstract     = {The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.},
  author       = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin},
  journal      = {Plant Cell},
  number       = {10},
  pages        = {3858 -- 3870},
  publisher    = {American Society of Plant Biologists},
  title        = {{Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid}},
  doi          = {10.1105/tpc.113.114421},
  volume       = {25},
  year         = {2013},
}

@article{516,
  abstract     = {In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.},
  author       = {Bargmann, Bastiaan and Vanneste, Steffen and Krouk, Gabriel and Nawy, Tal and Efroni, Idan and Shani, Eilon and Choe, Goh and Friml, Jirí and Bergmann, Dominique and Estelle, Mark and Birnbaum, Kenneth},
  journal      = {Molecular Systems Biology},
  number       = {1},
  publisher    = {Nature Publishing Group},
  title        = {{A map of cell type‐specific auxin responses}},
  doi          = {10.1038/msb.2013.40},
  volume       = {9},
  year         = {2013},
}

@article{522,
  abstract     = {Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic endothelial cells and responsible for separation of blood and lymphatic circulation through activation of platelets. Here we show that podoplanin is also expressed by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell type associated with thymic conduits, and involved in development of natural regulatory T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes in the medulla. This might be due to CCL21 that delocalizes upon deletion of the CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not remain devoid of nTreg but generate them delayed within the first month resulting in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype of Foxp3-deficient Scurfy mice.},
  author       = {Fuertbauer, Elke and Zaujec, Jan and Uhrin, Pavel and Raab, Ingrid and Weber, Michele and Schachner, Helga and Bauer, Miroslav and Schütz, Gerhard and Binder, Bernd and Sixt, Michael K and Kerjaschki, Dontscho and Stockinger, Hannes},
  journal      = {Immunology Letters},
  number       = {1-2},
  pages        = {31 -- 41},
  publisher    = {Elsevier},
  title        = {{Thymic medullar conduits-associated podoplanin promotes natural regulatory T cells}},
  doi          = {10.1016/j.imlet.2013.07.007},
  volume       = {154},
  year         = {2013},
}

@article{527,
  abstract     = {The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.},
  author       = {Wabnik, Krzysztof T and Robert, Hélène and Smith, Richard and Friml, Jirí},
  journal      = {Current Biology},
  number       = {24},
  pages        = {2513 -- 2518},
  publisher    = {Cell Press},
  title        = {{Modeling framework for the establishment of the apical-basal embryonic axis in plants}},
  doi          = {10.1016/j.cub.2013.10.038},
  volume       = {23},
  year         = {2013},
}

@article{528,
  abstract     = {Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14].},
  author       = {Robert, Hélène and Grones, Peter and Stepanova, Anna and Robles, Linda and Lokerse, Annemarie and Alonso, Jose and Weijers, Dolf and Friml, Jirí},
  journal      = {Current Biology},
  number       = {24},
  pages        = {2506 -- 2512},
  publisher    = {Cell Press},
  title        = {{Local auxin sources orient the apical basal axis in arabidopsis embryos}},
  doi          = {10.1016/j.cub.2013.09.039},
  volume       = {23},
  year         = {2013},
}

@article{2516,
  abstract     = {We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.},
  author       = {Lampert, Christoph and Nickisch, Hannes and Harmeling, Stefan},
  journal      = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  number       = {3},
  pages        = {453 -- 465},
  publisher    = {IEEE},
  title        = {{Attribute-based classification for zero-shot learning of object categories}},
  doi          = {10.1109/TPAMI.2013.140},
  volume       = {36},
  year         = {2013},
}

@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},
}

@misc{13075,
  abstract     = {Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.},
  author       = {Lohse, Konrad and Barton, Nicholas H and Stone, Graham and Melika, George},
  publisher    = {Dryad},
  title        = {{Data from: A likelihood-based comparison of population histories in a parasitoid guild}},
  doi          = {10.5061/DRYAD.0G0FS},
  year         = {2012},
}

@inproceedings{2048,
  abstract     = {Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively.},
  author       = {Faust, Sebastian and Pietrzak, Krzysztof Z and Schipper, Joachim},
  booktitle    = { Conference proceedings CHES 2012},
  location     = {Leuven, Belgium},
  pages        = {213 -- 232},
  publisher    = {Springer},
  title        = {{Practical leakage-resilient symmetric cryptography}},
  doi          = {10.1007/978-3-642-33027-8_13},
  volume       = {7428},
  year         = {2012},
}

@inproceedings{2049,
  abstract     = {We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.

Performance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.
},
  author       = {Heyse, Stefan and Kiltz, Eike and Lyubashevsky, Vadim and Paar, Christof and Pietrzak, Krzysztof Z},
  booktitle    = { Conference proceedings FSE 2012},
  location     = {Washington, DC, USA},
  pages        = {346 -- 365},
  publisher    = {Springer},
  title        = {{Lapin: An efficient authentication protocol based on ring-LPN}},
  doi          = {10.1007/978-3-642-34047-5_20},
  volume       = {7549},
  year         = {2012},
}

@inproceedings{1384,
  abstract     = {Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.},
  author       = {Beyer, Dirk and Henzinger, Thomas A and Keremoglu, Mehmet and Wendler, Philipp},
  booktitle    = {Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering},
  location     = {Cary, NC, USA},
  publisher    = {ACM},
  title        = {{Conditional model checking: A technique to pass information between verifiers}},
  doi          = {10.1145/2393596.2393664},
  year         = {2012},
}

@misc{5396,
  abstract     = {We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete  Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it  from training data. Experimental results show that for certain types of graphs a learned function can out-perform the  Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.},
  author       = {Korc, Filip and Kolmogorov, Vladimir and Lampert, Christoph},
  issn         = {2664-1690},
  pages        = {13},
  publisher    = {IST Austria},
  title        = {{Approximating marginals using discrete energy minimization}},
  doi          = {10.15479/AT:IST-2012-0003},
  year         = {2012},
}

@techreport{5398,
  abstract     = {This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers.},
  author       = {Porsche, Jana},
  publisher    = {IST Austria},
  title        = {{Actual state of research data @ ISTAustria}},
  year         = {2012},
}

@inbook{5745,
  author       = {Gupta, Ashutosh},
  booktitle    = {Automated Technology for Verification and Analysis},
  isbn         = {9783642333859},
  issn         = {1611-3349},
  location     = {Thiruvananthapuram, Kerala, India},
  pages        = {107--121},
  publisher    = {Springer Berlin Heidelberg},
  title        = {{Improved Single Pass Algorithms for Resolution Proof Reduction}},
  doi          = {10.1007/978-3-642-33386-6_10},
  volume       = {7561},
  year         = {2012},
}

@article{6588,
  abstract     = {First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.},
  author       = {Pausinger, Florian},
  issn         = {1812-9471},
  journal      = {Journal of Mathematical Physics, Analysis, Geometry},
  number       = {1},
  pages        = {63--78},
  publisher    = {B. Verkin Institute for Low Temperature Physics and Engineering},
  title        = {{Elementary solutions of the Bernstein problem on two intervals}},
  volume       = {8},
  year         = {2012},
}

@article{9451,
  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},
  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{9497,
  abstract     = {The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.},
  author       = {Coleman-Derr, Devin and Zilberman, Daniel},
  issn         = {1553-7404},
  journal      = {PLoS Genetics},
  number       = {10},
  publisher    = {Public Library of Science},
  title        = {{Deposition of histone variant H2A.Z within gene bodies regulates responsive genes}},
  doi          = {10.1371/journal.pgen.1002988},
  volume       = {8},
  year         = {2012},
}

@article{9499,
  abstract     = {EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.},
  author       = {Kim, Sang Yeol and Lee, Jungeun and Eshed-Williams, Leor and Zilberman, Daniel and Sung, Z. Renee},
  issn         = {1553-7404},
  journal      = {PLoS Genetics},
  number       = {3},
  publisher    = {Public Library of Science},
  title        = {{EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development}},
  doi          = {10.1371/journal.pgen.1002512},
  volume       = {8},
  year         = {2012},
}