LUKE/BI Plant Genome Dynamics

Institute of Biotechnology
LUKE/BI Plant Genome Dynamics
Biocentre 3, P.O. Box 65
Viikinkaari 1
00014 University of Helsinki
Finland

Tel +358-504483470
Fax +358-294159930

ProfessorDr. Alan H. Schulman

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Welcome to the Plant Genome Dynamics Lab

Retrotransposons: central players in the structure, evolution and function of eukaryotes

Complete understanding of the genome requires knowledge of both the role and function of the genes as well as the repetitive component, particularly regarding the dynamics of the retrotransposons. The genome of most higher eukaryotes is over 70% repetitive DNA, with estimates for the number of genes ranging from 10  to 50 thousand. In higher plants, more than half of the repetitive DNA consists of retrotransposons, a component dynamic by its ability to integrate new copies and facilitate to homologous recombination.

Introduction. Since the rediscovery of Mendel's laws of independent assortment, the establishment of genetic linkage as a property of chromosomes, and the discovery of the genetic code and molecular nature of the gene, two fundamental discoveries, apart from epigenetic phenomena such as imprinting, have changed our views of genetics: the existence of transposable elements, and the presence of repetitive DNA as the major component of the genome. Transposable elements, as self-mobilizing, independent genetic units, comprise a dynamic, fluid, rapidly evolving segment of the genome and in this way differ from traditional genes. Repetitive DNA, unlike the low-copy genes, generally does not encode traits which can be mapped by traditional recombinational genetics. It contributes to the so-called C-value paradox, whereby the DNA content, or coding capacity, of an organism in no way reflects the organism's complexity. The paradox has been resolved by the realization that the share of the genome dedicated to genes in relatively constant in the eukaryotes, whereas the amount of repetitive DNA, over 70% of the total, varies widely even within families of organisms.

Of the repetitive DNA in plants, a large proportion, in cereals >70%, is comprised of retrotransposons. Unlike the Type II DNA transposons, integrated copies are not excised and their transposition is replicative. Hence, each transcript of a retrotransposon has the formal potential to be integrated as cDNA back into the genome, giving rise to additional transcripts following integration. These new copies would be heritable if the integrations occurred in cells ultimately giving rise to gametes. It is therefore perhaps no surprise that in many genomes, particularly of plants, the retrotransposons are highly prevalent, contributing even half of the total DNA content. As such, they comprise a major part of the repetitive DNA component of the genome. The retrotransposons, as we have shown for gypsy-like elements and others for the copia-like, are ubiquitous in the plants and found in all other groups of organisms (as endogenous retroviruses in mammals). Their encoded gene products, organization, and mechanisms of mobility are also remarkably conserved. These classes are unlikely to have evolved multiple times; this implies that they were already in existence in the last common ancestor of the fungi, plants, and animals. The ancient, ubiquitous, prevalent, and dynamic nature of retrotransposons raises the question of their role and impact on organisms and their genes.

Basic research goals. The BARE-1 retrotransposon, which we discovered, is an especially active system, the only one to date demonstrated to be transcriptionally active in somatic tissues and translated, processed, and assembled into virus-like particles, the VLPs. It is a major, dispersed component of the genome and highly conserved in its functional domains. We have recently shown that BARE-1 is a major factor in genome size dynamics in barley and its genus Hordeum, and that intra-element recombination plays a major role in controlling genome expansion resulting from BARE-1 integration. As evolutionary opportunists, retrotransposon success depends on their interface with basic cellular processes including stress response and its signal transduction as well as the cell cycle. Hence, our basic goal is to understand the steps of retrotransposon replication, their regulated by the element and by the cell, and the impact of retrotransposons on the genome. To realize this goal, we are analyzing BARE-1 transcriptional control in various tissues to understand genetic fixation of newly integrated copies, determining the share of the BARE-1 family which is translationally competent, working out the steps of BARE-1 VLP assembly, and studying BARE-1 integration and target-site choice. We plan to determine the relative frequencies of integration and intra-element recombination, the ultimate balancing factor regulating BARE-1 copy number.

Applied research goals. Barley is an ideal research subject for retrotransposons. More importantly, however, it is the major crop in area and yield in Scandinavia. The Nordic region, and Europe more generally, faces the serious challenge of maintaining agricultural production in face of dwindling support and shifting consumer demands. Response to these demands requires the best possible germplasm on our farmers' fields. This requires that the available genetic resources need to be accessible to the plant breeders. The genetic diversity existing in genebanks must be introduced in the most efficient manner possible by conventional breeding methods. Our overall applied goal is to bring together three recently developed tools to meet this challenge. These are: retrotransposon-based molecular markers for marker-assisted breeding and map-based cloning; ESTs for gene discovery, phenotyping, expression profiling, recombinational mapping, and physical mapping; BACs (large-insert libraries for map-based cloning of candidate genes and physical mapping. We have developed three new and highly effective molecular marker techniques, IRAP, REMAP and iPBS, based on the insertional polymorphism generated by active retrotransposons. Retrotransposon-based molecular markers have considerable advantages over existing methods, as described in detail below. The REMAP, IRAP and iPBS system will give access to traits through high density recombinsational maps, the BACs through large, contiguous stretches of the genome, and ESTs through direct identification of genes of interest. These will be major enabling technologies for practical goals, such as our proposed map-based cloning of a net-blotch resistance gene, carried out in collaboration with plant breeders.