Developmental significance of epigenetic impositions on the plant genome: A paragenetic function for chromosomes

Developmental and physiological factors can impose heritable metastable changes on the plant genome, a fact that was established by maize geneticists during the 1950s and 1960s, largely through the efforts of R. Alexander Brink and Barbara McClintock. This paper describes a transgenic reporter system that monitors genomic impositions as changes in morphogenetically-determined flower color patterns. The observations reported here on the metastable properties of plant transgenes illustrate the proposals of Brink and McClintock that chromosomal impositions occur during normal development as ordered sequences of events which contribute to the elaboration of complex developmental patterns. The relationship between this process and some recent findings about the control of gene expression in transgenic plants is also discussed. © 1994 Wiley-Liss, Inc.     

Seeing Patterns: Models, Visual Evidence and Pictorial Communication in the Work of Barbara McClintock

Barbara McClintock won the Nobel Prize in 1983 for her discovery of mobile genetic elements. Her Nobel work began in 1944, and by 1950 McClintock began presenting her work on “controlling elements.” McClintock performed her studies through the use of controlled breeding experiments with known mutant stocks, and read the action of controlling elements (transposons) in visible patterns of pigment and starch distribution. She taught close colleagues to “read” the patterns in her maize kernels, “seeing” pigment and starch genes turning on and off. McClintock illustrated her talks and papers on controlling elements or transposons with photographs of the spotted and streaked maize kernels which were both her evidence and the key to her explanations. Transposon action could be read in the patterns by the initiated, but those without step by step instruction by McClintock or experience in maize often found her presentations confusing. The photographs she displayed became both McClintock's means of communication, and a barrier to successful presentation of her results. The photographs also had a second and more subtle effect. As images of patterns arrived at through growth and development of the kernel, they highlight what McClintock believed to be the developmental consequences of transposition, which in McClintock's view was her central contribution, over the mechanism of transposition, for which she was eventually recognized by others. Scientific activities are extremely visual, both at the sites of investigation and in communication through drawings, photographs, and movies. Those visual messages deserve greater scrutiny by historians of science. This revised version was published online in July 2006 with corrections to the Cover Date.     

Transposable elements as artisans of the heterochromatic genome in Drosophila melanogaster

Over 50 years ago Barbara McClintock discovered that maize contains mobile genetic elements, but her findings were at first considered nothing more than anomalies. Today it is widely recognized that transposable elements have colonized all eukaryotic genomes and represent a major force driving evolution of organisms. Our contribution to this special issue deals with the theme of transposable element-host genome interactions. We bring together published and unpublished work to provide a picture of the contribution of transposable elements to the evolution of the heterochromatic genome in Drosophila melanogaster. In particular, we discuss data on 1) colonization of constitutive heterochromatin by transposable elements, 2) instability of constitutive heterochromatin induced by the I factor, and 3) evolution of constitutive heterochromatin and heterochromatic genes driven by transposable elements. Drawing attention to these topics may have direct implications on important aspects of genome organization and gene expression.     

“The Real Point is Control”: The Reception of Barbara McClintock's Controlling Elements

In the standard narrative of her life, Barbara McClintock discovered genetic transposition in the 1940s but no one believed her. She was ignored until molecular biologists of the 1970s “rediscovered” transposition and vindicated her heretical discovery. New archival documents, as well as interviews and close reading of published papers, belie this narrative. Transposition was accepted immediately by both maize and bacterial geneticists. Maize geneticists confirmed it repeatedly in the early 1950s and by the late 1950s it was considered a classic discovery. But for McClintock, movable elements were part of an elaborate system of genetic control that she hypothesized to explain development and differentiation. This theory was highly speculative and was not widely accepted, even by those who had discovered transposition independently. When Jacob and Monod presented their alternative model for gene regulation, the operon, her controller argument was discarded as incorrect. Transposition, however, was soon discovered in microorganisms and by the late 1970s was recognized as a phenomenon of biomedical importance. For McClintock, the award of the 1983 Nobel Prize to her for the discovery of movable genetic elements, long treated as a legitimation, may well have been bittersweet. This new look at McClintock's experiments and theory has implications for the intellectual history of biology, the social history of American genetics, and McClintock's role in the historiography of women in science. This revised version was published online in July 2006 with corrections to the Cover Date.     

The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium

Heterochromatin, constitutively condensed chromosomal material, is widespread among eukaryotes but incompletely characterized at the nucleotide level. We have sequenced and analyzed 2.1 megabases (Mb) of Arabidopsis thaliana chromosome 4 that includes 0.5-0.7 Mb of isolated heterochromatin that resembles the chromosomal knobs described by Barbara McClintock in maize. This isolated region has a low density of expressed genes, low levels of recombination and a low incidence of genetrap insertion. Satellite repeats were absent, but tandem arrays of long repeats and many transposons were found. Methylation of these sequences was dependent on chromatin remodeling. Clustered repeats were associated with condensed chromosomal domains elsewhere. The complete sequence of a heterochromatic island provides an opportunity to study sequence determinants of chromosome condensation.     

A brief history of the status of transposable elements: from junk DNA to major players in evolution

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.     

Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus

The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize.     

Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay

Long Interspersed Elements (LINE-1s, L1s) are the most active mobile elements in the human genome and account for a significant fraction of its mass. The propagation of L1 in the human genome requires disruption and repair of DNA at the site of integration. As Barbara McClintock first hypothesized, genotoxic stress may contribute to the mobilization of transposable elements, and conversely, element mobility may contribute to genotoxic stress. We tested the ability of genotoxic agents to increase L1 retrotransposition in a cultured cell assay. We observed that cells exposed to gamma radiation exhibited increased levels of L1 retrotransposition. The L1 retrotransposition frequency was proportional to the number of phosphorylated H2AX foci, an indicator of genotoxic stress. To explore the role of the L1 endonuclease in this context, endonuclease-deficient tagged L1 constructs were produced and tested for their activity in irradiated cells. The activity of the endonuclease-deficient L1 was very low in irradiated cells, suggesting that most L1 insertions in irradiated cells still use the L1 endonuclease. Consistent with this interpretation, DNA sequences that flank L1 insertions in irradiated cells harbored target site duplications. These results suggest that increased L1 retrotransposition in irradiated cells is endonuclease dependent. The mobilization of L1 in irradiated cells potentially contributes to genomic instability and could be a driving force for secondary mutations in patients undergoing radiation therapy.     

Ongoing endeavors to detect mobilization of transposable elements

Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.     

Transposons,environmental changes,and heritable induced phenotypic variability

The mechanisms of biological evolution have always been, and still are, the subject of intense debate and modeling. One of the main problems is how the genetic variability is produced and maintained in order to make the organisms adaptable to environmental changes and therefore capable of evolving. In recent years, it has been reported that, in flies and plants, mutations in Hsp90 gene are capable to induce, with a low frequency, many different developmental abnormalities depending on the genetic backgrounds. This has suggested that the reduction of Hsp90 amount makes different development pathways more sensitive to hidden genetic variability. This suggestion revitalized a classical debate around the original Waddington hypothesis of canalization and genetic assimilation making Hsp90 the prototype of morphological capacitor. Other data have also suggested a different mechanism that revitalizes another classic debate about the response of genome to physiological and environmental stress put forward by Barbara McClintock. That data demonstrated that Hsp90 is involved in repression of transposon activity by playing a significant role in piwi-interacting RNA (piRNAs)-dependent RNA interference (RNAi) silencing. The important implication is that the fixed phenotypic abnormalities observed in Hsp90 mutants are probably related to de novo induced mutations by transposon activation. In this case, Hsp90 could be considered as a mutator. In the present theoretical paper, we discuss several possible implications about environmental stress, transposon, and evolution offering also a support to the concept of evolvability.     

Are Probabilities Necessary For Evolutionary Explanations?

Several philosophers of science have advanced an instrumentalist thesis about the use of probabilities in evolutionary biology. I investigate the consequences of instrumentalism on evolutionary explanations. I take issue with Barbara Horan's (1994) argument that probabilities are unnecessary to explain evolutionary change given the underlying deterministic character of evolutionary processes. First, I question Horan's deterministic assumption. Then, I attempt to undermine her Laplacian argument by demonstrating that whether probabilities are necessary depends upon the sort of questions one is asking.     

Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification

Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.     

An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice

While characterized mutable alleles caused by DNA transposons have been abundant in maize since the discovery of Dissociation conferring variegation by Barbara McClintock, only a few mutable alleles have been described in rice even though the rice genome contains various transposons. Here, we show that a spontaneous mutable virescent allele, pyl-v, is caused by the disruption of the nuclear-coded essential chloroplast protease gene, OsClpP5, due to insertion of a 607-bp non-autonomous DNA transposon, non-autonomous DNA-based active rice transposon one (nDart1), belonging to the hAT superfamily. The transposition of nDart1 can be induced by crossing with a line containing an autonomous element, aDart, and stabilized by segregating out of aDart. We also identified a novel mutable dwarf allele thl-m caused by an insertion of nDart1. The japonica cultivar Nipponbare carries no aDart, although it contains epigenetically silenced Dart element(s), which can be activated by 5-azacytidine. Nipponbare bears four subgroups of about 3.6-kb Dart-like sequences, three of which contain potential transposase genes, and around 3.6-kb elements without an apparent transposase gene, as well as three subgroups of about 0.6-kb nDart1-related elements that are all internal deletions of the Dart-like sequences. Both nDart1 and 3.6-kb Dart-like elements were also present in indica varieties 93-11 and Kasalath. nDart1 appears to be the most active mutagen among nDart1-related elements contributing to generating natural variations. A candidate for an autonomous element, aDart, and a possible application of nDart1 for transposon tagging are discussed.     

The evolutionary origins of patriarchy

This article argues that feminist analyses of patriarchy should be expanded to address the evolutionary basis of male motivation to control female sexuality. Evidence from other primates of male sexual coercion and female resistance to it indicates that the sexual conflicts of interest that underlie patriarchy predate the emergence of the human species. Humans, however, exhibit more extensive male dominance and male control of female sexuality than is shown by most other primates. Six hypotheses are proposed to explain how, over the course of human evolution, this unusual degree of gender inequality came about. This approach emphasizes behavioral flexibility, cross-cultural variability in the degree of partriarchy, and possibilities for future change. This work was supported in part by NSF grant BNS-8857969. Barbara Smuts is a professor of psychology and anthropology at the University of Michigan. She received her B.A. in social anthropology at Harvard and her Ph.D. in bio-behavioral sciences at Stanford Medical School. She has studied the behavior of wild chimpanzees, baboons, and bottlenose dolphins and is particularly interested in evolutionary, comparative analyses of female-male relationships.     

VARIATION IN NITROGEN PHYSIOLOGY AND GROWTH AMONG GEOGRAPHICALLY ISOLATED POPULATIONS OF THE GIANT KELP,MACROCYSTIS PYRIFERA (PHAEOPHYTA)1

Three geographically isolated populations of the giant kelp, Macrocystis pyrifera (L.) C. Ag., were examined for responses to nitrate availability in batch culture experiments using juvenile sporophytes reared from spores in the laboratory. Although maximum rates of nitrate-saturated growth were similar among groups, there were significant quantitative differences in the response to nitrate limitation that can be related to natural patterns of nutrient availability at these sites. Plants from Santa Catalina Island (most oligotrophic) achieved maximum growth rates at ambient nitrate concentrations that were lower than those for plants from Monterey Bay, California (most eutrophic), or Refugio State Beach (near Santa Barbara, California). Tissue nitrogen and amino acid concentrations were highest in plants cultured from Santa Catalina Island populations at all external nitrate concentrations, suggesting that differences in nitrate requirements for growth may reflect the efficiency of nitrate uptake and assimilation at subsaturating nitrate concentrations. Given the different physical environments from which these plants came, the data suggest that geographically isolated populations of M. pyrifera have undergone genetic divergence that can be explained by ecotypic adaptation to unique habitat conditions at these sites.     

The physiology and pathology of inositide signaling in the nucleus

Nuclear inositide signaling is nowadays a well‐established issue and a growing field of investigation, even though the very first evidence came out at the end of the 1980's. The understanding of its biological role is supported by the recent acquisitions dealing with pathology and namely hematological malignancies. Here, we review this issue highlighting the main achievements in the last years. J. Cell. Physiol. 226: 14–20, 2010. © 2010 Wiley‐Liss, Inc.     

MORPHOLOGICAL VARIATION AND DEVELOPMENT IN RAMALINA MENZIESII TAYL.

The common west coast lichen Ramalina menziesii Tayl. has been studied in an attempt to determine the extent of morphological variation and to understand the factors that determine its form. An analysis of a typical population near Santa Barbara, CA, suggested that intrapopulation variation in form was controlled primarily by size increase during growth. Test populations obtained from latitudes as far north as 54°N and as far south as 28°N had values for various morphological characters that were very similar to the Santa Barbara population. It is concluded that variation in form may be the result of differential rates of growth and possibly varying frequency of environmental stresses which disintegrate the thallus.