• About
    Introduction
    Our research at CINVESTAV-Irapuato focuses on the epigenetic mechanisms of gene regulation in plants of agronomic importance, in the study of genes involved in the priming phenomenon, and in the interaction Plant-Pathogen. Current research is performed in the common bean (Phaseolus vulgaris), tomato (Solanum lycopersicum), and on the model plant Arabidopsis.
    Current Institution
    Mexico City
    Current position
    Center for Research and Advanced Studies of the National Polytechnic Institute
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    Research Experience
    Jan 2007
    Principal Investigator
    Center for Research and Advanced Studies of the National Polytechnic Institute · Departamento de Ingeniería Genética (Irapuato)
    Irapuato, Mexico
    Description
    P.I.
    May 2005 - Dec 2006
    Pioneer Hi-Bred Production, Ltd.
    Ontario, Canada
    Description
    Posdoc
    Jun 2002 - Apr 2005
    University of Nebraska at Lincoln · Department of Biological Sciences
    Lincoln, USA
    Description
    Posdoc
    Education
    Aug 1995 - May 2002
    Purdue University
    Biochemistry and Molecular Biology
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    Awards & Achievements (2)
    Jan 2015
    National Researcher, category SNI 2
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    Jan 2008
    National Researcher, category SNI 1
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    Projects (1)
    Project
    Priming phenomenon in the common bean
    Research
    Research Items (65)
    Question - How many papers related to pharmacogenetics were produced in 2016, around the world?
    Answer
    A "Pharmacogenetics" search at NCBI/PubMed = 1197 articles, for the year 2016.
    Question - Has anybody used the CRISPR/Cas9 system to insert eukaryotic telomeric repeats into telomeric regions?
    Answer
    Thank you. Very helpful. 
    Project - Study of the priming phenomenon in the common bean
    Update
    Deleted research item The research item mentioned here has been deleted
    Throughout evolution, plants have developed diverse mechanisms of defense that “prime” their innate immune system for more robust and active induction of defense responses against different types of stress. Nowadays there are numerous reports concerning the molecular bases of priming, as well as the generational priming mechanisms. Information concerning transgenerational priming, however, remains deficient. Some reports have indicated, nonetheless, that the priming status of a plant can be inherited to its offspring. Here, we show that the priming agent b-aminobutyric acid induced resistance to Pseudomonas syringae pv. phaseolicola infection in the common bean (Phaseolus vulgaris L.) We have analyzed the transgenerational patterns of gene expression of the PvPR1 gene (Phaseolus vulgaris PR1), a highly responsive gene to priming, and show that a transgenerational priming response against pathogen attack can last for at least two generations. We hypothesize that a defense-resistant phenotype and easily identifiable, generational and transgenerational, “primed patterns” of gene expression are excellent indicators of the priming response in crop plants. Furthermore, we propose here that modern plant breeding methods and crop improvement efforts must include the use of elicitors to prime induced resistance in the field and, above all, to select for induced heritable states in progeny that is primed for defense.
    About this Research Topic: Epigenetics is a new field that explains gene expression at the chromatin structure and organization level. Three principal epigenetic mechanisms are known and hundreds of combinations among them can develop different phenotypic characteristics. DNA methylation, histone modifications and small RNAs have been identified, and their functions are being studied in order to understand the mechanisms of interaction and regulation among the different biological processes in plants. Although, fundamental epigenetic mechanisms in crop plants are beginning to be elucidated, the comprehension of the different epigenetic mechanisms, by which plant gene regulation and phenotype are modified, is a major topic to develop in the near future in order to increase crop productivity. Thus, the importance of epigenetics in improving crop productivity is undoubtedly growing. Current research on epigenetics suggest that DNA methylation, histone modifications and small RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, defense response and plant growth. The aim of this Research Topic is to explore the recent advances concerning the role of epigenetics in crop biotechnology, as well as to enhance and promote interactions among high quality researchers from different disciplines such as genetics, cell biology, pathology, microbiology, and evolutionary biology in order to join forces and decipher the epigenetic mechanisms in crops productivity.
    To survive in adverse conditions, plants have evolved complex mechanisms that “prime” their defense system to respond and adapt to stresses. Their competence to respond to such stresses fundamentally depends on its capacity to modulate the transcriptome rapidly and specifically. Thus, chromatin dynamics is a mechanism linked to transcriptional regulation and enhanced defense in plants. For example, in Arabidopsis, priming of the SA-dependent defense pathway is linked to histone lysine methylation. Such modifications could create a memory of the primary infection that is associated with an amplified gene response upon exposure to a second stress-stimulus. In addition, the priming status of a plant for induced resistance can be inherited to its offspring. However, analyses on the molecular mechanisms of generational and transgenerational priming in the common bean (Phaseolus vulagris L.), an economically important crop, are absent. Here, we provide evidence that resistance to P. syringae pv. phaseolicola infection was induced in the common bean with the synthetic priming activators BABA and INA. Resistance was assessed by evaluating symptom appearance, pathogen accumulation, changes in gene expression of defense genes, as well as changes in the H3K4me3 and H3K36me3 marks at the promoter-exon regions of defense-associated genes. We conclude that defense priming in the common bean occurred in response to BABA and INA and that these synthetic activators primed distinct genes for enhanced disease resistance. We hope that an understanding of the molecular changes leading to defense priming and pathogen resistance will provide valuable knowledge for producing disease-resistant crop varieties by exposing parental plants to priming activators, as well as to the development of novel plant protection chemicals that stimulate the plant's inherent disease resistance mechanisms.
    Histone methylation profiles of the P. vulgaris genes involved in plant defense at various days after germination (dag). Plants were primed with activators and later inoculated with P. syringae pv. phaseolicola (Activator + P.s.), inoculated only (no activator + P.s.), or neither primed nor inoculated (control, ctrl). ChIP assays with antibodies specific for H3K36me3 in BABA-primed and INA-primed plants. Depletion of H3K36me3 from the promoter-exon boundary region correlates with enhanced transcription of the primed genes. Two independent biological assays are shown.
    Transcript levels in F1 progeny of selected genes involved in plant defense. Progeny were either: unprimed and not inoculated (−) or unprimed and inoculated with P. syringae pv. phaseolicola (− + P.s.). F1 progeny were descended from F0 plants that had been primed with activator and inoculated with P. syringae pv. phaseolicola (Activator + P.s.), inoculated only (− + P.s.), or neither primed nor inoculated (Ctrl 1 or 2). Data were normalized to the elongation factor 1-α (PvEF1α) reference gene. Data represent mean ± SD, n = 3 independent experiments. Statistical significance for the F1 generation was determined with multiple Student's t-test, followed by the Holm-Šídák multiple comparison test at a significance value of 0.05, by using the GraphPad Prism (v 6.0, GraphPad Software, San Diego California USA, http://www.graphpad.com). A one-way ANOVA with Dunnett's post-test was performed using GraphPad Prism (v 6.0, GraphPad Software, San Diego California USA) at a significance value of 0.05 (see Supplementary Table 2).
    Multiple Student's t-test analysis, followed by the Holm-Šídák multiple comparison test at a significance value of 0.05. Statistically significant values are in bold letters.
    One-way ANOVA with Dunnett's post test at a significance value of 0.05. Statistically significant values are in bold.
    Transcript levels of selected genes involved in plant defense in P. vulgaris plants as determined by end-point PCR. Plants were primed with activators (BABA- or INA-treated plants) followed by inoculation with P. syringae pv. phaseolicola (Activator + P.s.), inoculated only (no activator + P.s.), or neither primed nor inoculated (control, ctrl). Data represents the densitometric analysis of defense-related gene expression. PvActin11 was used as a control for each template preparation and was amplified under exactly the same conditions as the tested genes. Dag, days after germination.
    Transcript levels of genes from P. vulgaris involved in plant defense as determined by qRT-PCR at various days after germination (dag). Plants were primed with activators (BABA- or INA-treated plants) followed by inoculation with P. syringae pv. phaseolicola (Activator + P.s.), inoculated only (no activator + P.s.), or neither primed nor inoculated (control, ctrl). Data were normalized to the elongation factor 1-α (PvEF1α) reference gene. Data represent mean ± SD, n = 3 independent experiments. Statistical significance for the F0 generation was determined with multiple Student's t-test, followed by the Holm-Šídák multiple comparison test at a significance value of 0.05, by using the GraphPad Prism (v 6.0, GraphPad Software, San Diego California USA, http://www.graphpad.com) (see Supplementary Table 1).
    Histone methylation profiles as determined by ChIP assays with antibodies specific for H3K36me3. F1 progeny were descended from F0 plants that had been primed with activator and inoculated with P. syringae pv. phaseolicola (Activator + P.s.), inoculated only (− + P.s.), or neither primed nor inoculated (Ctrl). Two independent biological assays are shown.
    It is now known that epigenetic modifications control gene expression by modulating the access of regulatory complexes to the genome. Furthermore, current research on epigenetic mechanisms indicate that DNA methylation, histone posttranslational modifications and small non-coding RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, and plant immunity. Even though the basic epigenetic mechanisms in crop biotechnology are starting to be uncovered, soon they will be extensively employed for crop improvement and to increase crop productivity in challenge environments. This research Topic includes an excellent combination of Mini Reviews, Reviews, Original Research Articles, and Methods focused on the role of epigenetics in crop biotechnology, and provides up-to-date information on epigenetics in crop plants during in vitro culture, abiotic and biotic stresses, and gene silencing.
    Question
    The authors wish to draw the attention to two irregularities in Figures 2a and 4. Both concern errors in duplicating images of "empty" lanes illustrating absence of DNA bands. We regret these omissions and apologize to readers for the inconvenience caused. The results and conclusions remain valid.
    2015). The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell 20: 568–579. Figure 7C (WRKY70 ChIP-PCR assay) has been corrected to clarify that the wild-type control sample for H3K4m3 was run on a separate gel from the atx1 and atx2 samples, indicated by the space (white line, bottom row). The samples for H3K4m2 (top row) were run together on the same gel. The legend and labeling on the figure have been amended slightly for clarity. The original conclusions of the manuscript are unaltered by these corrections. Editor's note: the corrected figure and accompanying text were reviewed by members of The Plant Cell editorial board. Figure 7. Original: Expression and H3K4 Methylation Patterns of WRKY70 in Wild-Type, atx1, and atx2 Chromatin. (C) WRKY70 amplified from ChIP assays of wild-type, atx1, and atx2 flower chromatin immunoprecipitated with antibodies distinguishing between di-and trimethylated H3K4 isoforms. Labeling is as in Figure 5C. A schematic illustration of the WRKY70 gene including the regions amplified for the ChIP assay is shown at top of the panel. Figure 7. Corrected: Expression and H3K4 Methylation Patterns of WRKY70 in Wild-Type, atx1, and atx2 Chromatin. (C) WRKY70 amplified from ChIP assays of wild-type, atx1, and atx2 flower chromatin immunoprecipitated with antibodies distinguishing between di-and trimethylated H3K4 isoforms. The control wild-type samples for H3K4m3, separated by a space (white line in the bottom panel), were resolved in a different gel from atx1 and atx2 samples. The blots were developed and processed in parallel. I, input sample representing 10% of the template amount used for the immunoprecipitation. 2Αb and 1Ab are immunoprecipitated chromatins without and with added antibody, respectively. A schematic illustration of the WRKY70 gene including the regions amplified for the ChIP assay is shown at top of the panel. www.plantcell.org/cgi/
    Question - How does one perform a chromatin accessibility assay in plants nuclei extract with Micrococcal nuclease digestion?
    Answer
    Yes you can. Check these articles. They might help you:
    1) Gévry N, Svotelis A, Larochelle M, Gaudreau L. 2009. Nucleosome Mapping. En: Tom Moss and Benoît Leblanc (eds.), Methods in Molecular Biology, DNA-Protein Interactions, vol. 543; chapter 19. Humana Press, DOI: 10.1007/978-1-60327-015-1_19
    2) Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants. Zhang T, Zhang W, Jiang J. Plant Physiol. 2015 Aug;168(4):1406-16. doi: 10.1104/pp.15.00125. Epub 2015 Jul 4.
    Histone methylation is a conserved epigenetic mechanism in eukaryotes. Most of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for enzymatic activity. Genetic studies in Arabidopsis thaliana have revealed that proteins from the Trithorax group (TrxG) are critical in activating transcription by methylating lysine 4 and lysine 36 of histone H3. Two TrxG proteins, ATXR3 and ATX1 (also called SET DOMAIN GROUP 2 and 27, respectively) are necessary for global genome-wide H3K4me3 deposition in Arabidopsis, whilst ASHH2 (also called SDG8) is a multi-functional enzyme with H3K4 and H3K36 methylation activity. Using phylogenetic analysis, we have identified the common bean (Phaseolus vulgaris L.) gene orthologs to Arabidopsis ATXR3, ASHH2, and ATX1 genes, which we have designated PvATXR3h, PvASHH2h, and PvTRX1h, respectively. Analysis of these genes with qRT-PCR reveals that all three are broadly expressed during plant and nodule development. Through a reverse genetics approach, we created common bean composite plants to knock-down PvATXR3h, PvTRX1h, and PvASHH2h expression. From analysis of the transgenic root phenotype, we conclude that transgenic root growth and development in the common bean was hindered by PvASHH2h gene downregulation.
    Common bean is the most important grain legume in the human diet. Bean improvement efforts have been focused on classical breeding techniques because bean is recalcitrant to both somatic embryogenesis and in vitro regeneration. This study was undertaken to better understand the process of somatic embryogenesis in the common bean. We focused on the mechanisms by which somatic embryogenesis in plants is regulated and the interaction of these mechanisms with plant hormones. Specifically, we examined the role of the gene PvTRX1h, an ortholog of a major known histone lysine methyltransferase in plants, in somatic embryo generation. Given the problems with regeneration and transformation, we chose to develop and use regeneration-competent callus that could be successively transformed. Embryogenic calli of common bean were generated and transformed with the PvTRX1hRiA construction to down-regulate, by RNA interference, expression of the PvTRX1h gene. Plant hormone content was measured by mass spectrometry and gene expression was assessed by q-PCR. Detailed histological analysis was performed on selected transgenic embryogenic calli. It was determined that down-regulation of PvTRX1h gene was accompanied by altered concentrations of plant hormones in the calli. PvTRX1h regulated the expression of genes involved in auxin biosynthesis and embryogenic calli in which PvTRX1h was down-regulated were capable of differentiation into somatic embryos. Also, down-regulation of PvTRX1h showed increased transcript abundance of a gene coding for a second histone lysine methyltransferase, PvASHH2h. Accordingly, the PvTRX1h gene is involved in the synthesis of plant hormones in common bean callus. These results shed light on the crosstalk among histone methyltransferases and plant hormone signaling and on gene regulation during somatic embryo generation.
    Common bean is the most important grain legume in the human diet. Bean improvement efforts have been focused on classical breeding techniques because bean is recalcitrant to both somatic embryogenesis and in vitro regeneration. This study was undertaken to better understand the process of somatic embryogenesis in the common bean. We focused on the mechanisms by which somatic embryogenesis in plants is regulated and the interaction of these mechanisms with plant hormones. Specifically, we examined the role of the gene PvTRX1h, an ortholog of a major known histone lysine methyltransferase in plants, in somatic embryo generation. Given the problems with regeneration and transformation, we chose to develop and use regeneration-competent callus that could be successively transformed. Embryogenic calli of common bean were generated and transformed with the PvTRX1hRiA construction to down-regulate, by RNA interference, expression of the PvTRX1h gene. Plant hormone content was measured by mass spectrometry and gene expression was assessed by q-PCR. Detailed histological analysis was performed on selected transgenic embryogenic calli. It was determined that down-regulation of PvTRX1h gene was accompanied by altered concentrations of plant hormones in the calli. PvTRX1h regulated the expression of genes involved in auxin biosynthesis and embryogenic calli in which PvTRX1h was down-regulated were capable of differentiation into somatic embryos. Also, down-regulation of PvTRX1h showed increased transcript abundance of a gene coding for a second histone lysine methyltransferase, PvASHH2h. Accordingly, the PvTRX1h gene is involved in the synthesis of plant hormones in common bean callus. These results shed light on the crosstalk among histone methyltransferases and plant hormone signaling and on gene regulation during somatic embryo generation.
    Question - Is there anyone in mexico working with the fungus Fusarium oxysporum f . sp. nicotianae and bacteria Pseudomonas syringae DC3000 strain?
    Answer
    Hola Angeles. Puedes enviarme un e-mail a mi correo institucional para comentar al respecto. Saludos. Raúl
    Question - While doing VIGS, can the infiltrated virus spread from the leaves to the germline tissues and knockdown the germline gene?
    Answer
    Yes. Just do the VIGS. It is better if you use particle gun bombardment.
    Ciclos de reproducción cortos y la oportunidad de incrementar la ganancia genética, junto con el estudio de las bases moleculares de la vernalización, son áreas esenciales de investigación dentro de la biología de plantas. Varios métodos se han empleado para lograr el silenciamiento génico en plantas, pero ninguno reportado a la fecha para canola (Brassica napus), y en particular para inducir la floración sin vernalización en líneas de invierno a través del uso de secuencias sentido de DNA en vectores diseñados para el silenciamiento génico inducido por virus (VIGS). La presente investigación provee los métodos para transitoriamente regular a la baja, por medio de VIGS, genes de la vernalización en plantas anuales de invierno, específicamente la familia de genes de Flowering Locus C (FLC) en canola de invierno (BnFLC1 a BnFLC5). La regulación a la baja de estos genes permite a las plantas anuales de invierno florecer sin vernalización y, consecuentemente, provee los medios para acelerar la ganancia genética. El sistema de silenciamiento propuesto puede ser utilizado para regular a la baja familias de genes, para determinar la función génica, y para inducir la floración sin la vernalización en líneas de invierno tanto del género Brassica como de muchos cultivos importantes de invierno.
    Genetic studies along with biochemical and cell biological analyses in plant model systems have enabled researchers to understand how proteins are recruited to chromatin and how they regulate their target genes and to elucidate their functions. Accordingly, it has become evident that a majority of human genes that were suspected or known to play a role in disease had orthologs in the model plant Arabidopsis thaliana and many other plants (like the common bean, Phaseolus vulgaris L.). Also, it is now recognized that many disease and defense responsive mechanisms in Arabidopsis appear to be under epigenetic control, analogous to roles played by animal Polycomb Group/Trithorax Group (PcG/Trx) complexes in the regulation of senescence, disease and cancer, though it is not clear how plant pathogens manipulate, for example, host post-translational modifications (PTMs) and how they use these PTMs to solve their own biological requirements. While it has become clear in recent years that many stress responses involve epigenetic components, we are far from understanding the mechanisms and molecular interactions. Extending our knowledge is fundamental, not least for plant breeding and conservation biology. Grain legumes, and particularly the common bean (Phaseolus vulgaris L.), are known to be recalcitrant towards in vitro regeneration. Consequently, genetic transformation is hard to achieve for this organism. Therefore, it is crucial the development of an efficient method for the creation and establishment of regeneration-competent callus and its transformation, as a first step towards an efficient plant regeneration system and genetic transformation in P. vulgaris. In addition, the establishment of a chromatin state required for inducible defense against pathogens (‘priming’), and how to manipulate the epigenetic processes involved in the interaction plant-microorganism are key points in order to improve future plant breeding and crop productivity.
    ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1/SDG27), a known regulator of flower development, encodes a H3K4histone methyltransferase that maintains a number of genes in an active state. In this study, the role of ATX1 in root development was evaluated. The loss-of-function mutant atx1-1 was impaired in primary root growth. The data suggest that ATX1 controls root growth by regulating cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation. In atx1-1, the quiescent centre (QC) cells were irregular in shape and more expanded than those of the wild type. This feature, together with the atypical distribution of T-divisions, the presence of oblique divisions, and the abnormal cell patterning in the RAM, suggests a lack of coordination between cell division and cell growth in the mutant. The expression domain of QC-specific markers was expanded both in the primary RAM and in the developing lateral root primordia of atx1-1 plants. These abnormalities were independent of auxin-response gradients. ATX1 was also found to be required for lateral root initiation, morphogenesis, and emergence. The time from lateral root initiation to emergence was significantly extended in the atx1-1 mutant. Overall, these data suggest that ATX1 is involved in the timing of root development, stem cell niche maintenance, and cell patterning during primary and lateral root development. Thus, ATX1 emerges as an important player in root system architecture.
    Over the past decades, chromatin remodelling has emerged as an important regulator of gene expression and plant defense. This book provides a detailed understanding of the epigenetic mechanisms involved in plants of agronomic importance. The information presented here is significant because it is expected to provide the knowledge needed to develop in the future treatments to manipulate and selectively activate/inhibit proteins and metabolic pathways to counter pathogens, to treat important diseases and to increase crop productivity. New approaches of this kind and the development of new technologies will certainly increase our knowledge of currently known post-translational modifications and facilitate the understanding of their roles in, for example, hostpathogen interactions and crop productivity. Furthermore, we provide important insight on how the plant epigenome changes in response to developmental or environmental stimuli, how chromatin modifications are established and maintained, to which degree they are used throughout the genome, and how chromatin modifications influence each other
    Over the past decades, chromatin remodelling has emerged as an important regulator of gene expression and plant defense. This book provides a detailed understanding of the epigenetic mechanisms involved in plants of agronomic importance. The information presented here is significant because it is expected to provide the knowledge needed to develop in the future treatments to manipulate and selectively activate/inhibit proteins and metabolic pathways to counter pathogens, to treat important diseases and to increase crop productivity. New approaches of this kind and the development of new technologies will certainly increase our knowledge of currently known post-translational modifications and facilitate the understanding of their roles in, for example, host-pathogen interactions and crop productivity. Furthermore, we provide important insight on how the plant epigenome changes in response to developmental or environmental stimuli, how chromatin modifications are established and maintained, to which degree they are used throughout the genome, and how chromatin modifications influence each another. © 2014 Springer International Publishing Switzerland. All rights reserved.
    Question - How important is RNAse and Proteinase K treatment in ChIP assays?
    Answer
    Hi,
    I do not use RNAse with my ChIP assays (no columns). But, might help.
    To revert cross-linking I add 5 M NaCl and incubate at 65 oC for at least 4 h.
    I also believe that the proteinase K treatment is important with the reverse cross linking, I always use it (1h at 45oC).
    Good luck!
    Question - How do you access published raw epigenetic data?
    Answer
    Hi,
    Check the Chromatin Database:
    Could help.
    Question - What is the role of PRC complexes in plant gene silencing?
    Answer
    Hi,
    Check these articles. You might get an answer here:
    PRC1
    1.
    Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes.
    Molitor AM, Bu Z, Yu Y, Shen WH.
    PLoS Genet. 2014 Jan;10(1):e1004091. doi: 10.1371/journal.pgen.1004091. Epub 2014 Jan 23.
    2.
    Mechanisms guiding Polycomb activities during gene silencing in Arabidopsis thaliana.
    He C, Huang H, Xu L.
    Front Plant Sci. 2013 Nov 13;4:454. doi: 10.3389/fpls.2013.00454. Review.
    3.
    PRC1 marks the difference in plant PcG repression.
    Calonje M.
    Mol Plant. 2014 Mar;7(3):459-71. doi: 10.1093/mp/sst150. Epub 2013 Oct 31.
    4.
    The polycomb complex PRC1: composition and function in plants.
    Molitor A, Shen WH.
    J Genet Genomics. 2013 May 20;40(5):231-8. doi: 10.1016/j.jgg.2012.12.005. Epub 2013 Jan 3. Review.
    PRC2
    5.
    Genomic imprinting in the Arabidopsis embryo is partly regulated by PRC2.
    Raissig MT, Bemer M, Baroux C, Grossniklaus U.
    PLoS Genet. 2013 Dec;9(12):e1003862. doi:…
    Question - How can I search for the gene sequence of histone demethylase "jumonji 8" in Arabidopsis?
    Answer
    HI,
    If you do a search at the NCBI, this is what you get from Arabidopsis. However, jumonji 8 is from animals, I believe (see at the end genes). so you have to find the ortholog in Arabidopsis. Hopefully this will help.
    Arabidopsis:
    Select item 821629AT3G20810
    ID: 821629
    jumonji-C domain-containing protein 30 [Arabidopsis thaliana (thale cress)] Chromosome 3, NC_003074.8 (7275674..7278379) AT3G20810
    Select item 839963AT1G30810
    ID: 839963
    jumonji domain-containing protein 18 [Arabidopsis thaliana (thale cress)] Chromosome 1, NC_003070.9 (10936765..10942292, complement) AT1G30810T17H7.10, T17H7_10
    Select item 834736AT5G46910
    ID: 834736
    transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana (thale cress)] Chromosome 5, NC_003076.8 (19046858..19050880) AT5G46910MQD22.4, MQD22_4
    Select item 837747AT1G11950
    ID: 837747
    transcription factor jumonji (jmjC) domain-containing protein [Arabidopsis thaliana (thale cress)] Chromosome 1, NC_003070.9…
    Question - What are the epigenetic consequences of maternal folic acid supplementation?
    Answer
    Hi,
    You might find some answers in the following articles:
    1.
    Maternal exposure to fluoxetine during gestation and lactation affects the DNA methylation programming of rat's offspring: modulation by folic acid supplementation.
    Toffoli LV, Rodrigues GM Jr, Oliveira JF, Silva AS, Moreira EG, Pelosi GG, Gomes MV.
    Behav Brain Res. 2014 May 15;265:142-7. doi: 10.1016/j.bbr.2014.02.031. Epub 2014 Feb 28.
    2.
    Single-base resolution of mouse offspring brain methylome reveals epigenome modifications caused by gestational folic acid.
    Barua S, Kuizon S, Chadman KK, Flory MJ, Brown WT, Junaid MA.
    Epigenetics Chromatin. 2014 Feb 3;7(1):3. doi: 10.1186/1756-8935-7-3.
    3.
    Impact of folic acid fortification on global DNA methylation and one-carbon biomarkers in the Women's Health Initiative Observational Study cohort.
    Bae S, Ulrich CM, Bailey LB, Malysheva O, Brown EC, Maneval DR, Neuhouser ML, Cheng TY, Miller JW, Zheng Y, Xiao L, Hou L, Song X, Buck K, Beresford SA, Caudill MA.
    Epigenetics. 2014 Mar;9(3):396-403.…
    Question - Where can I find papers on Epigenetics in Chronic Diseases & Aging?
    Answer
    Hi,
    If you do a search at the NCBI you will get the following articles. Hopefuly it will help:
    1.
    Stem cells as vehicles for youthful regeneration of aged tissues.
    Rando TA, Wyss-Coray T.
    J Gerontol A Biol Sci Med Sci. 2014 Jun;69 Suppl 1:S39-42. doi: 10.1093/gerona/glu043.
    PMID: 24833585 [PubMed - in process]
    Related citations
    Select item 24795656
    2.
    Meditation as a Therapeutic Intervention for Adults at Risk for Alzheimer's Disease - Potential Benefits and Underlying Mechanisms.
    Innes KE, Selfe TK.
    Front Psychiatry. 2014 Apr 23;5:40. eCollection 2014. Review.
    PMID: 24795656 [PubMed - as supplied by publisher] Free PMC Article
    Related citations
    Select item 24789982
    3.
    Beyond the genome: epigenetic mechanisms in lung remodeling.
    Hagood JS.
    Physiology (Bethesda). 2014 May;29(3):177-85. doi: 10.1152/physiol.00048.2013.
    PMID: 24789982 [PubMed - in process]
    Related citations
    Select item 24527405
    4.
    Epigenetic regulation in allergic diseases and related studies.
    Kuo CH, Hsieh CC, Lee MS, Chang KT, Kuo HF, Hung CH.
    Question - How to draw nucleosomal array?
    Question - What role do environmental factors play in the genesis of schizophrenia?
    Answer
    Hi,
    Take a look at the research done by Suzanne King of McGill University. You'll find here her publications: http://www.mcgill.ca/tcpsych/faculty/suzanneking.
    Also see:
    Selected Articles
    Brenner, K., St-Hilaire, A., Liu, A., Laplante D. P., & King, S. (2011). Cortisol response and coping style predict quality of life in schizophrenia. Schizophrenia Research. Advance online publication. doi:10.1016/j.schres.2011.01.016
    King, S., St-Hilaire, A., & Heidkamp, D. (2010). A review of prenatal factors in schizophrenia. Current Directions in Psychological Science, 19(4), 209–213.
    Charil, A., Laplante D. P., Vaillancourt, C., & King, S. (2010). Prenatal maternal stress and brain development. Brain Research Reviews, 65, 56-79.
    King, S., Mancini-Marïe, A., Brunet, A., Walker, E. F., Meaney, M. J., & Laplante, D. P. (2009). Prenatal maternal stress from a natural disaster predicts dermatoglyphic asymmetry in humans. Development & Psychopathology, 21, 343-353.
    Brenner, K , Liu, A., Laplante, D. P.,…
    Plant hormones, or phytohormones, are a structurally unrelated collection of small molecules derived from various essential metabolic pathways, which act at low concentrations to regulate the plant growth and development, as well as their response to biotic and abiotic stresses. Even thought plant chromatin as well as plant hormone signalling are areas of great significance, the studies related to the effect of plant hormones on plant chromatin pattern are scarce, along with research dealing with chromatin modifications, or chromatin modifiers, involved in phytohormone biosynthesis. Grain legumes, and particularly the common bean (Phaseolus vulgaris L.), are known to be recalcitrant towards in vitro regeneration. Consequently, genetic transformation is hard to achieve for this organism. Therefore, it is imperative the development of an efficient method for the creation and establishment of regeneration-competent callus and its transformation, as a first step towards an efficient plant regeneration system and genetic transformation in P. vulgaris. In this study, we were able to generate embryogenic callus of P. vulgaris, and transformed them by particle gun bombardment, in order to investigate the role of PvTRX1h gene, an ortholog to a major known histone lysine methyltransferase in plants. We assessed the effects of down-regulation of PvTRX1h in pro-embryogenic callus. Our findings show that by down-regulating PvTRX1h: pro-embryogenic calluses are able to form somatic embryos with diverse phenotypes; an over production of somatic embryos is achieved; the concentration of the different plant hormones in the common bean calluses changed significantly and can be associated to the phenotypes seen; and vTRX1h regulates expression of genes involved in the synthesis of phytohormones. This research provides the knowledge needed to build the foundation for the generation of transgenic somatic embryos with the further potential to regenerate transgenic common bean plants, and in turn, to increase crop productivity for this grain legume.
    It has been shown by many researchers that SET-domain containing proteins modify chromatin structure and, as expected, genes coding for SET-domain containing proteins have been found in all eukaryotic genomes sequenced to date. However, during the last years, a great number of bacterial genomes have been sequenced and an important number of putative genes involved in histone post-translational modifications (histone PTMs) have been identified in many bacterial genomes. Here, I aim at presenting an overview of SET domain genes that have been identified in numbers of bacterial genomes based on similarity to SET domains of eukaryotic histone methyltransferases. I will argue in favor of the hypothesis that SET domain genes found in extant bacteria are of bacterial origin. Then, I will focus on the available information on pathogen and symbiont SET-domain containing proteins and their targets in eukaryotic organisms, and how such histone methyltransferases allow a pathogen to inhibit transcriptional activation of host defense genes.
    Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations ('promiscuous' domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements ('cassettes'). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms.
    Neighbor-Joining phylogeny of PWWP containing proteins in A. thaliana.
    The genes encoding the PWWP domain containing proteins in A. thaliana and in A. lyrata.
    Multiple sequence alignments used for generating the phylogenetic trees in this study.
    Neighbor-Joining phylogeny of PWWP containing proteins in plants including the ATX3-like protein from O. tauri and the ATX1-like protein of Chlamydomonas.
    Phylogeny of the 12 taxa included in the study.
    Gene architecture of the PWWP domain containing proteins from the 12 genomes studied.
    Maximum Likelihood phylogeny of PWWP containing proteins in A. thaliana.
    Neighbor-Joining phylogeny of PWWP containing proteins in humans, Nematostella, M. brevicolis and O. tauri .
    Polycomb group (PcG) and trithorax group (trxG) proteins are key regulators of homeotic genes and have central roles in cell proliferation, growth and development. In animals, PcG and trxG proteins form higher order protein complexes that contain SET domain proteins with histone methyltransferase activity, and are responsible for the different types of lysine methylation at the N-terminal tails of the core histone proteins. However, whether H3K4 methyltransferase complexes exist in Arabidopsis thaliana remains unknown. Here, we make use of the yeast two-hybrid system and the bimolecular fluorescence complementation assay to provide evidence for the self-association of the Arabidopsis thaliana SET-domain-containing protein SET DOMAIN GROUP 26 (SDG26), also known as ABSENT, SMALL, OR HOMEOTIC DISCS 1 HOMOLOG 1 (ASHH1). In addition, we show that the ASHH1 protein associates with SET-domain-containing sequences from two distinct histone lysine methyltransferases, the ARABIDOPSIS HOMOLOG OF TRITHORAX-1 (ATX1) and ASHH2 proteins. Furthermore, after screening a cDNA library we found that ASHH1 interacts with two proteins from the heat shock protein 40 kDa (Hsp40/DnaJ) superfamily, thus connecting the epigenetic network with a system sensing external cues. Our findings suggest that trxG complexes in Arabidopsis thaliana could involve different sets of histone lysine methyltransferases, and that these complexes may be engaged in multiple developmental processes in Arabidopsis.
    In eukaryotes, trithorax group proteins play critical roles in the regulation of transcription, cell proliferation, differentiation and development. In this work we report the molecular cloning and characterization of two cDNAs, PvuTRX1h and PvuASH1h, from the common bean Phaseolus vulgaris, both of which encode polypeptides homologues of trithorax group members described in animals and yeast. A full length clone of PvuTRX1h was isolated from total RNA prepared from roots and consisting of a 3270 bp ORF encoding 1089 amino acids, while the PvuAsh1h consists of a 1446 bp ORF encoding 481 amino acids. Characterization of the isolated sequences revealed that they contain all the canonical domains present in proteins from the TRX (trithorax) and ASH1 families. A comparison of the PvuTRX1h and PvuASH1h SET-domain sequences with homologous proteins from plants, animals and yeast, revealed that PvuTRX1h is phylogenetically related to the TRX family of histone lysine methyltransferases while PvuASH1h clusters with members of the ASH1 family. Quantitative RT-PCR (reverse transcription polymerase chain reaction) analyses of transcript abundance in roots and nodules, at different developmental stages, demonstrated that PvuTRX1h is particularly abundant at early stages of nodule development, whereas PvuASH1h functions at the stages of highest nitrogen-fixing activity of the nodules, suggesting that these genes could be involved in the formation of nitrogen-fixing nodules in P. vulgaris. This work reports the presence and characterization of Trithorax-group homolog genes in P. vulgaris and their expression patterns during nodule development.
    Genes in eukaryotic organisms function within the context of chromatin, and the mechanisms that modulate the structure of chromatin are defined as epigenetic. In Arabidopsis, pathogen infection induces the expression of at least one histone deacetylase, suggesting that histone acetylation/deacetylation has an important role in the pathogenic response in plants. How/whether histone methylation affects gene response to pathogen infection is unknown. To gain a better understanding of the epigenetic mechanisms regulating the interaction between Pseudomonas syringae and Arabidopsis thaliana, we analysed three different Arabidopsis ash1-related (absent, small or homeotic discs 1) mutants. We found that the loss of function of ASHH2 and ASHR1 resulted in faster hypersensitive responses (HRs) to both mutant (hrpA) and pathogenic (DC3000) strains of P. syringae, whereas control (Col-0) and ashr3 mutants appeared to be more resistant to the infection after 2 days. Furthermore, we showed that, in the ashr3 background, the PR1 gene (PATHOGENESIS-RELATED GENE 1) displayed the highest expression levels on infection with DC3000, correlating with increased resistance against this pathogen. Our results show that, in both the ashr1 and ashh2 backgrounds, the histone H3 lysine 4 dimethylation (H3K4me2) levels decreased at the promoter region of PR1 on infection with the DC3000 strain, suggesting that an epigenetically regulated PR1 expression is involved in the plant defence. Our results suggest that histone methylation in response to pathogen infection may be a critical component in the signalling and defence processes occurring between plants and microbes.
    Shorter breeding cycles and the opportunity for enhanced genetic gains, together with the study of the molecular basis of vernalization, are essential areas of research in plant biology. Several approaches have been employed to achieve gene silencing in plants, but none so far reported in canola (Brassica napus), and particularly to induce flowering without vernalization in true winter lines by using sense DNA sequences in virus-induced gene silencing (VIGS) vectors. The present research provides the methods to transiently down-regulate, by VIGS technology, vernalization genes in winter annuals, specifically the family of Flowering Locus C (FLC) genes in winter canola (BnFLC1 to BnFLC5). Down-regulation of the BnFLC genes allows winter annuals to flower without vernalization and consequently provides the means for enhanced genetic gains. The proposed silencing system can be used to down-regulate gene families, to determine gene function, and to induce flowering without vernalization in winter Brassica lines as well as in many important winter crops.
    Resulta imperativo incluir un componente filogenético explícito al concepto y medida de la biodiversidad, con la idea de que la filogenética es una de las herramientas más eficaces para establecer las áreas críticas que requieren de un sólido manejo ambiental y con el fin de proteger el proceso activo de la evolución contemporánea.
    Polycomb group (PcG) and trithorax group (trxG) proteins are key regulators of homeotic genes and have crucial roles in cell proliferation, growth and development. PcG and trxG proteins form higher order protein complexes that contain SET domain proteins, with a histone methyltransferase (HMTase) activity, responsible for the different types of lysine methylation at the N-terminal tails of the core histone proteins. In recent years, genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to begin to understand how PcG and trxG proteins are recruited to chromatin and how they regulate their target genes and to elucidate their functions. This review focuses on the advances in our understanding of the biological roles of PcG and trxG proteins, their molecular mechanisms of action and further examines the role of histone marks in PcG and trxG regulation in Arabidopsis.
    The present invention provides nucleic acid molecules and methods to down-regulate by virus-induced gene silencing (VIGS) vernalization genes in Winter annuals, specifically the Flowering Locus C (FLC) gene in Brassica napus. Down regulation of FLC allows winter annuals to flower without vemalization or with reduced vernalization. This, in turn, provides a shorter breeding cycling and the opportunity for enhanced genetic gain.
    Mechanisms that chemically modify nucleosomes leading to inheritable activation or repression of pertinent genes are defined as epigenetic. H3K4me3 and H3K27me3 are interpreted as 'activating' and 'silencing' marks, respectively. Here, we demonstrate that even for related genes neither modification, alone, could serve as an indicator of expression status: despite being members of the same gene family selectively activated by ATX1, FLC and AP1 nucleosomes may be similarly decorated but, also, surprisingly different. 'Activating' H3K4me3 and 'silencing' H3K27me3 modifications co-exist at 5'-end nucleosomes of transcriptionally active FLC-gene, while highly transcribed AP1 displays neither of the two marks. The results suggest that distinct mechanisms 'read' and operate at each locus. In a remarkable contrast, H3K4me3-H3K27me3 profiles at downstream FLC and AP1 gene sequences remain unchanged and transmitted as stable marks throughout development. We propose that H3K4me3 and H3K27me3 produce a distinct bi-modular 'syllable' in the histone 'code' conveying different meaning on specific genes. Evidence that certain chromatin modifications might be common for active or non-active genome regions but, also, that the same histone signs might have gene-specific 'meaning', as reported here, might be critically important for large-scale genome analyses. ATX1 and CLF encode enzyme activities involved in establishing the H3K4me3 and H3K27me3 marks, respectively. The potential involvement of ATX1 and CLF in generating the dual H3K4me3 and H3K27me3 marks on FLC and AP1 nucleosomes was investigated.
    Gene duplication followed by functional specialization is a potent force in the evolution of biological diversity. A comparative study of two highly conserved duplicated genes, ARABIDOPSIS TRITHORAX-LIKE PROTEIN1 (ATX1) and ATX2, revealed features of both partial redundancy and of functional divergence. Although structurally similar, their regulatory sequences have diverged, resulting in distinct temporal and spatial patterns of expression of the ATX1 and ATX2 genes. We found that ATX2 methylates only a limited fraction of nucleosomes and that ATX1 and ATX2 influence the expression of largely nonoverlapping gene sets. Even when coregulating shared targets, ATX1 and ATX2 may employ different mechanisms. Most remarkable is the divergence of their biochemical activities: both proteins methylate K4 of histone H3, but while ATX1 trimethylates it, ATX2 dimethylates it. ATX2 and ATX1 provide an example of separated K4 di from K4 trimethyltransferase activity.
    Chromatin immunoprecipitation (ChIP) is a powerful tool for the characterization of covalent histone modifications and DNA-histone interactions in vivo. The procedure includes DNA-histone cross-linking in chromatin, shearing DNA into smaller fragments, immunoprecipitation with antibodies against the histone modifications of interest, followed by PCR identification of associated DNA sequences. In this protocol, we describe a simplified and optimized version of ChIP assay by reducing the number of experimental steps and isolation solutions and shortening preparation times. We include a nuclear isolation step before chromatin shearing, which provides a good yield of high-quality DNA resulting in at least 15 mug of DNA from each immunoprecipitated sample (from 0.2 to 0.4 g of starting tissue material) sufficient to test > or =25 genes of interest. This simpler and cost-efficient protocol has been applied for histone-modification studies of various Arabidopsis thaliana tissues and is easy to adapt for other systems as well.
    The expression of the Arabidopsis gene WRKY70 is known to be antagonistically regulated by the salicylic acid (SA) and jasmonic acid (JA) signaling pathways. The gene encodes a transcription factor functioning at the crossroad of the two pathways. Here we show that the Arabidopsis homolog of Trithorax, ATX1, activates the expression of the WRKY70 gene and is involved in establishing the trimethylation pattern of histone H3 tail lysine 4 (H3K4me3) residues of its nucleosomes. Chromatin immunoprecipitation (ChIP) analyses with antiATX1 specific antibodies demonstrated that WRKY70 is a primary target for the ATX1 histone methylase activity, while the SA-responsive gene, PR1, and the JA-responsive gene, THI2.1, are secondary targets. The unexpected finding that PR1 and THI2.1 nucleosomes carryH3K4me3-marks unrelated to their transcription states suggests that the defense-response genes PR1 and THI2.1 keep their nucleosomes in 'actively' modified state, perhaps, in preparation for quick-changes of transcription when needed by the cell. Based on the experimental data, we propose a model that could explain the ability of a single epigenetic factor to orchestrate expression of a large number of genes, particularly in cases involving response reactions.
    The presence of Supressor of variegation-Enhanser of zeste-Trithorax (SET) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. Because a major function of SET domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial SET domain genes. Consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was taken as evidence that bacteria have obtained the SET domain genes from their hosts. Furthermore, it was proposed that the products of the genes would, most likely, be involved in bacteria–host interactions. The broadened scope of sequenced bacterial genomes to include also free-living and environmental species provided a larger sample to analyze the bacterial SET domain genes. By phylogenetic analysis, examination of individual chromosomal regions for signs of insertion, and evaluating the chromosomal versus SET domain genes' GC contents, we provide evidence that SET domain genes have existed in the bacterial domain of life independently of eukaryotes. The bacterial genes have undergone an evolution of their own unconnected to the evolution of the eukaryotic SET domain genes. Initial finding of SET domain genes in predominantly pathogenic and symbiotic bacteria resulted, most probably, from a biased sample. However, a lateral transfer of SET domain genes may have occurred between some bacteria and a family of Archaea. A model for the evolution and distribution of SET domain genes in bacteria is proposed.
    Tightly balanced antagonism between the Polycomb group (PcG) and the Trithorax group (TrxG) complexes maintain Hox expression patterns in Drosophila and murine model systems. Factors belonging to the PcG/TrxG complexes control various processes in plants as well but whether they participate in mechanisms that antagonize, balance or maintain each other's effects at a particular gene locus is unknown. CURLY LEAF (CLF), an Arabidopsis homolog of enhancer of zeste (EZ) and the ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) control the expression of the flower homeotic gene AGAMOUS (AG). Disrupted ATX1 or CLF function results in misexpression of AG, recognizable phenotypes and loss of H3K4me3 or H3K27me3 histone H3-tail marks, respectively. A novel idea suggested by our results here, is that PcG and TrxG complexes function as a specific pair generating bivalent chromatin marks at the silent AG locus. Simultaneous loss of ATX1 and CLF restored AG repression and normalized leaf phenotypes. At the molecular level, disrupted ATX1 and CLF functions did not lead to erasure of the CLF- and ATX1-generated epigenetic marks, as expected: instead, in the double mutants, H3K27me3 and H3K4me3 tags were partially restored. We demonstrate that ATX1 and CLF physically interact linking mechanistically the observed effects.
    Phosphoinositide phosphates, PtdInsP, are important components of the cell lipid pool that can function as messengers in diverse cellular processes. Lack of information on downstream targets, however, has impeded our understanding of the potential of lipid-signaling to influence gene activity. Our goals here were to identify genes that altered expression in the presence of two isomeric monophosphate lipid messengers (Phosphoinositide 5-Phosphate, PtdIns(5)P, and Phosphoinositide 4-Phosphate, PtdIns(4)P) and to establish whether the two lipids influence distinct or overlapping gene-sets. Our results indicated that PtdIns(5)P and PtdIns(4)P affected genes within shared gene-families but that each messenger influenced the expression of different members within the same family. These results suggested that PtdIns(5)P and PtdIns(4)P participate in separate pathways that, ultimately, may control gene expression. The pathways may have points of convergence but may also counteract each other's effects. A significant fraction ( approximately 40%) of the PtdIns(5)P-stimulated genes belong to various families of wall-modifying genes. Wall-modifying activities are recognized as factors affecting cell extension and plant growth. Elevated PtdIns(5)P concentration influenced stem growth and the effects were different from those triggered by PtdIns(4)P. The data allow insights into plants' response to two related PtdInsP at whole-plant/genome-wide levels and demonstrate that PtdIns(5)P-and PtdIns(4)P-involving mechanisms are distinct, selective and specific.
    The Arabidopsis homolog of trithorax, ATX1, regulates numerous functions in Arabidopsis beyond the homeotic genes. Here, we identified genome-wide targets of ATX1 and showed that ATX1 is a receptor for a lipid messenger, phosphatidylinositol 5-phosphate, PI5P. PI5P negatively affects ATX1 activity, suggesting a regulatory pathway connecting lipid-signaling with nuclear functions. We propose a model to illustrate how plants may respond to stimuli (external or internal) that elevate cellular PI5P levels by altering expression of ATX1-controlled genes. • epigenetic regulation • lipid signaling
    Covalent modifications of histone-tail amino acid residues communicate information via a specific ‘histone code’. Here, we report histone H3-tail lysine methylation profiles of several Arabidopsis genes in correlation with their transcriptional activity and the input of the epigenetic factor ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) at ATX1-regulated loci. By chromatin immunoprecipitation (ChIP) assays, we compared modification patterns of a constitutively expressed housekeeping gene, of a tissue-specific gene, and among genes that differed in degrees of transcriptional activity. Our results suggest that the di-methylated isoform of histone H3-lysine4 (m2K4/H3) provide a general mark for gene-related sequences distinguishing them from non-transcribed regions. Lys-4 (K4/H3), lys-9 (K9/H3) and lys-27 (K27/H3) nucleosome methylation patterns of plant genes may be gene-, tissue- or development-regulated. Absence of nucleosomes from the LTP-promotor was not sufficient to provoke robust transcription in mutant atx1-leaf chromatin, suggesting that the mechanism repositioning nucleosomes at transition to flowering functioned independently of ATX1.
    The genes of the trithorax (trxG) and Polycomb groups (PcG) are best known for their regulatory functions in Drosophila, where they control homeotic gene expression. Plants and animals are thought to have evolved multicellularity independently. Although homeotic genes control organ identity in both animals and plants, they are unrelated. Despite this fact, several plant homeotic genes are negatively regulated by plant genes similar to the repressors from the animal PcG. However, plant-activating regulators of the trxG have not been characterized. We provide genetic, molecular, functional, and biochemical evidence that an Arabidopsis gene, ATX1, which is similar to the Drosophila trx, regulates floral organ development. The effects are specific: structurally and functionally related flower homeotic genes are under different control. We show that ATX1 is an epigenetic regulator with histone H3K4 methyltransferase activity. This is the first example of this kind of enzyme activity reported in plants, and, in contrast to the Drosophila and the yeast trithorax homologs, ATX1 can methylate in the absence of additional proteins. In its ability to methylate H3K4 as a recombinant protein, ATX1 is similar to the human homolog. ATX1 functions as an activator of homeotic genes, like Trithorax in animal systems. The histone methylating activity of the ATX1-SET domain argues that the molecular basis of these effects is the ability of ATX1 to modify chromatin structure. Our results suggest a conservation of trxG function between the animal and plant kingdoms despite the different structural nature of their targets.
    The finding in animal species of complexes homologous to the products of six Saccharomyces cerevisiae genes, origin of replication recognition complex (ORC), has suggested that ORC‐related mechanisms have been conserved in all eukaryotes. In plants, however, the only cloned putative homologs of ORC subunits are the Arabidopsis ORC2 and the rice ORC1. Homologs of other subunits of plant origin have not been cloned and characterized. A striking observation was the absence from the Arabidopsis genome of an obvious candidate gene‐homolog of ORC4. This fact raised compelling questions of whether plants, in general, and Arabidopsis, in particular, may have lost the ORC4 gene, whether ORC‐homologous subunits function within a complex in plants, whether an ORC complex may form and function without an ORC4 subunit, whether a functional (but not sequence) protein homolog may have taken up the role of ORC4 in Arabidopsis, and whether lack of ORC4 is a plant feature, in general. Here, we report the first cloned and molecularly characterized five genes coding for the maize putative homologs of ORC subunits ZmORC1, ZmORC2, ZmORC3, ZmORC4 and ZmORC5. Their expression profiles in tissues with different cell‐dividing activities are compatible with a role in DNA replication. Based on the potential of ORC‐homologous maize proteins to bind each other in yeast, we propose a model for their possible assembly within a maize ORC. The isolation and molecular characterization of an ORC4‐homologous gene from maize argues that, in its evolution, Arabidopsis may have lost the homologous ORC4 gene.
    Our major source of information on the mechanisms involved in processes regulating cell fate and developmental programs has been acquired from studies in animals. Plant homologs of the trithorax genes, as antagonists of Polycomb group genes, have not been characterized yet. We have isolated two Arabidopsis genes (ATX1 and ATX2 ), as first examples of plant genes of the Trithorax family. They are highly similar but display different tissue and development expression patterns. ATX1 was ubiquitously expressed with highest levels registered in young seedlings. ATX2 was less active in all tested tissues, was not expressed in mature leaves but was highly expressed in roots. Despite the high level of homology between them, their expression pattern in the various tissues tested and at different developmental stages suggested different functions for the two genes. ATX1 positively regulates the flower homeotic genes APETALA1, APETALA2, PISTILLATA and AGAMOUS , and is responsible for maintaining the levels of their mRNAs in immature flowers. Mutant atx1 Arabidopsis plants have impaired growth and homeotic floral alterations, suggesting developmental functions for the gene. ATX1 is defined as an activator of flower homeotic genes. The effects of ATX1 are highly specific. Like the animal counterpart, ATX1 does not appear to be involved in establishing an active state for the homeotic genes, but rather in maintaining it. This is the first evidence of the pleiotropic function of an Arabidopsis homolog of trithorax . We have defined a new structural domain in the molecular structure of ATX1 and ATX2. The possible function of this motif (DAST) has not been elucidated yet but, interestingly, DAST was found in genes of animal and plant origin only and is not present in bacteria and in yeast. We have systematized and comprehensively analyzed the currently available genes of three families, SU(VAR)3-9, E(Z), and TRITHORAX. This whole-genome comparative approach outlined an informative picture of a significant heterogeneity inside each family, unexpected relationships among same-family members and a tight correlation between the level of amino acid homology of the SET domain and the evolution of the entire architecture of any given gene. Alvarez-Venegas, R. (2002). Putative gene homologues of trithorax in arabidopsis (Order No. 3099120). Available from ProQuest Dissertations & Theses Global. (305507517). Retrieved from http://search.proquest.com/docview/305507517?accountid=27954
    SET-domain (SET: Su(var)3-9, E(z) and Trithorax)-containing proteins were collected through sequence searches of the available databases. After removing redundancies, the proteins belonging to three families, SU(VAR)3-9, E(Z) and Trithorax, were selected. Analysis of the relationship between the different members is based on pairwise alignment, compilation, and comparison of their SET-domains. The level of homology of the SET-domains defined the distribution of the proteins into families and into clades within the families. The architecture of the entire protein supported the distribution pattern built upon SET-domain similarity. Parallel cladistic and protein-architecture analyses outlined two plausible criteria for predicting function.
    Two Arabidopsis genes have been characterized as first examples of plant genes homologous to the animal trithorax genes. The Arabidopsis genes are highly similar but display different tissue and development expression patterns. One of them was ubiquitously expressed, with highest levels registered in young seedlings. The other gene was less active in all tested tissues, was not expressed in mature leaves but was highly expressed in roots. A new structural motif common to all TRX-related proteins has been identified. This new architectural element was found only in genes of multicellular species and is present in all genes belonging to the trithorax family. Along with the SET domain and the PHD fingers, this new element is a signature feature for the trithorax gene family.
    The purpose of this work was to evaluate the effects of germination on the nutritional quality of two commercial varieties of low tannin content Sorghum: brown sorghum without testa (ICSY-CM89513) and white sorghum (ISIAP Dorado). After 24 hours of germination the condensed tannin concentration (catechin equivalent) was reduced 60% and 40% for brown and white sorghum respectively. However, tannin levels increased up 100% at 96 h germination. Phytic acid concentration decreased about 90% in 96 hours for both varieties. The lysine concentration increased up 110% (72 h germination) and 129% (48 h) for white and brown sorghum respectively. The thiamine, niacin and riboflavin contents increased 73, 200 and 353% respectively for brown sorghum in 72 h and 15, 44 and 93% respectively for white sorghum in 48 h. The "in vitro" enzymatic digestibility was increased 39.3% (72 h) for brown sorghum and 100% for white sorghum. The albumin concentration increased 80% and 74% (72 h) for brown and white sorghum respectively. The Calculated Protein Efficiency Ratio indicated nutritional improvements with germination. The sprouting was a practical and simple process for providing better nutritional properties in sorghum seeds to be used as human food.
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