Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

/pdf/gene-ontology-tool-for-the-unification-of-biology-ppsktrcye3.pdf

Gene Ontology: tool for the unification of biology

A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes. Because of the small format and high density of the arrays, hybridization volumes of 2 microliters could be used that enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA. Differential expression measurements of 45 Arabidopsis genes were made by means of simultaneous, two-color fluorescence hybridization.

https://science.sciencemag.org/content/sci/270/5235/467.full.pdf

Quantitative monitoring of gene expression patterns with a complementary DNA microarray.

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

/pdf/analysis-of-the-genome-sequence-of-the-flowering-plant-3vizsb52m2.pdf

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Cells of a multicellular organism are genetically homogeneous but structurally and functionally heterogeneous owing to the differential expression of genes. Many of these differences in gene expression arise during development and are subsequently retained through mitosis. Stable alterations of this kind are said to be 'epigenetic', because they are heritable in the short term but do not involve mutations of the DNA itself. Research over the past few years has focused on two molecular mechanisms that mediate epigenetic phenomena: DNA methylation and histone modifications. Here, we review advances in the understanding of the mechanism and role of DNA methylation in biological processes. Epigenetic effects by means of DNA methylation have an important role in development but can also arise stochastically as animals age. Identification of proteins that mediate these effects has provided insight into this complex process and diseases that occur when it is perturbed. External influences on epigenetic processes are seen in the effects of diet on long-term diseases such as cancer. Thus, epigenetic mechanisms seem to allow an organism to respond to the environment through changes in gene expression. The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research.

/pdf/epigenetic-regulation-of-gene-expression-how-the-genome-55fnpf16ec.pdf

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

The discovery that mammalian cells have the ability to synthesize the free radical nitric oxide (NO) has stimulated an extraordinary impetus for scientific research in all the fields of biology and medicine. Since its early description as an endothelial-derived relaxing factor, NO has emerged as a fundamental signaling device regulating virtually every critical cellular function, as well as a potent mediator of cellular damage in a wide range of conditions. Recent evidence indicates that most of the cytotoxicity attributed to NO is rather due to peroxynitrite, produced from the diffusion-controlled reaction between NO and another free radical, the superoxide anion. Peroxynitrite interacts with lipids, DNA, and proteins via direct oxidative reactions or via indirect, radical-mediated mechanisms. These reactions trigger cellular responses ranging from subtle modulations of cell signaling to overwhelming oxidative injury, committing cells to necrosis or apoptosis. In vivo, peroxynitrite generation represents a crucial pathogenic mechanism in conditions such as stroke, myocardial infarction, chronic heart failure, diabetes, circulatory shock, chronic inflammatory diseases, cancer, and neurodegenerative disorders. Hence, novel pharmacological strategies aimed at removing peroxynitrite might represent powerful therapeutic tools in the future. Evidence supporting these novel roles of NO and peroxynitrite is presented in detail in this review.

/pdf/nitric-oxide-and-peroxynitrite-in-health-and-disease-3uuuqgfdcz.pdf

Nitric Oxide and Peroxynitrite in Health and Disease

Plants must carefully time the switch from vegetative growth to floral production in order to take advantage of optimal environmental conditions. In their Perspective, [Bastow and Dean][1] discuss new work ([ He et al .][2]) that reveals an elegant mechanism, involving chromatin remodeling of a genetic locus encoding a flowering repressor, which enables plants to regulate flowering time.

 [1]: http://www.sciencemag.org/cgi/content/full/302/5651/1695
 [2]: http://www.sciencemag.org/cgi/content/short/302/5651/1751

http://science.sciencemag.org/content/sci/302/5651/1695.full.pdf

Deciding when to flower

Analysis of how seasonal cues influence the timing of the floral transition has revealed many important principles for how epigenetic regulation can integrate a variety of environmental cues with developmental signals. The study of the pathways that necessitate overwintering in plants and their ability to respond to prolonged cold (the vernalization requirement and response pathways) has elaborated different chromatin regulatory pathways and the involvement of noncoding RNAs. The major target of these vernalization pathways in Arabidopsis (Arabidopsis thaliana )i sFlowering Locus C (FLC). A relatively simple picture of FLC regulation is emerging of a few core complexes and mechanisms that antagonize each other’s actions. This balance provides a fine degree of control that has nevertheless permitted evolution of a wide range of natural variation in vernalization in Arabidopsis. Similar simple routes of adaptation may underlie life history variation between species. The time at which different species flower is an important marker of seasonal and climatic changes and is ecologically and economically important. The sessile nature of plants means that they experience the full range of environmental changes over the seasons. Flowering time control in many species is highly responsive to environmental cues and therefore very sensitive to local climate conditions. The impact of this on many ecosystem and agricultural processes has made understanding flowering time control an important objective. Many genetic pathways influence flowering time, either as part of seasonal (photoperiod and past and present temperature), developmental (developmental phase and age), or stress response (overcrowding and nutrient stress). Despite the variety of competing inputs, these many and various mechanisms are integrated at the action of a small number of nodes in Arabidopsis (Arabidopsis thaliana) termed floral pathway integrators (Simpson and Dean, 2002). Analyses of the genes identified by flowering time mutants have shown many have roles as chromatin modifiers (Andres an dC oupland, 2012; Pajoro et al., 2014). Timing of flowering seems particularly sensitive to chromatin regulation, potentially due to the necessity for long-term storage of seasonal information. In this review, we focus on vernalization in Arabidopsis and summarize our understanding of how chromatin modifiers interact with other proteins and noncoding RNAs to integrate developmental and temperature cues into chromatin changes at the key integrating locus Flowering Locus C (FLC). Further, we explore how changes in these mechanisms underlie different life history strategies and vernalization responses in different accessions and species. A key observation we wish to convey is that the complexity of these systems at the molecular level belies simplicity in balancing forces that enable a fine degree of control and adaptive responses at the phenotypic level.

Flowering Locus C's Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation 1

Arabidopsis thaliana (Arabidopsis) has been adopted by a large number of plant biologists as the model organism in which to use a molecular genetic approach to dissect many plant processes. The small genome size of Arabidopsis and the concentration of effort on this plant species has led to an international collaboration to construct a physical map of the genome. The physical map will greatly facilitate gene isolation without the need for each laboratory to initiate chromosome walks. This, in combination with the development of efficient insertional mutagenesis systems, will mean that in the next few years the number of genes cloned from Arabidopsis will increase enormously.

Advantages of Arabidopsis for cloning plant genes

Analysis of the molecular basis of vernalization inArabidopsis thaliana

The maize transposable element Ac is highly active in the heterologous hosts tobacco and tomato, but shows very much reduced levels of activity in Arabidopsis. A mutagenesis experiment was undertaken with the aim of identifying Arabidopsis host factors responsible for the observed low levels of Ac activity. Seed from a line carrying a single copy of the Ac element inserted into the streptomycin phosphotransferase (SPT) reporter fusion, and which displayed typically low levels of Ac activity, were mutagenized using gamma rays. Nineteen mutants displaying high levels of somatic Ac activity, as judged by their highly variegated phenotypes, were isolated after screening the M2 generation on streptomycin-containing medium. The mutations fall into two complementation groups, iae1 and iae2, are unlinked to the SPT::Ac locus and segregate in a Mendelian fashion. The iae1 mutation is recessive and the iae2 mutation is semi-dominant. The iae1 and iae2 mutants show 550- and 70-fold increases, respectively, in the average number of Ac excision sectors per cotyledon. The IAE1 locus maps to chromosome 2, whereas the SPT::Ac reporter maps to chromosome 3. A molecular study of Ac activity in the iae1 mutant confirmed the very high levels of Ac excision predicted using the phenotypic assay, but revealed only low levels of Ac re-insertion. Analyses of germinal transposition in the iae1 mutant demonstrated an average germinal excision frequency of 3% and a frequency of independent Ac re-insertions following germinal excision of 22%. The iae mutants represents a possible means of improving the efficiency of Ac/Ds transposon tagging systems in Arabidopsis, and will enable the dissection of host involvement in Ac transposition and the mechanisms employed for controlling transposable element activity.

Caroline Dean

Papers

Deciding when to flower

Flowering Locus C's Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation 1

Advantages of Arabidopsis for cloning plant genes

Analysis of the molecular basis of vernalization inArabidopsis thaliana

Increased Ac excision (iae): Arabidopsis thaliana mutations affecting Ac transposition