Department of Biology

Research Projects of Dr Trude Schwarzacher

Molecular Cytogenetics Homepage

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Completed Projects
Early events of meiosis
Termini of chromosomes
Genomic in situ hybridization
Meiotic genes

Metaphase I of rye showing three ring and four rod bivalents

Genome organization and epigenetic mechanisms in polyploid plant species

Most estimates suggest that 50% of plant species are recognisable and evolutionary recent polyploids where diploid ancestors can be identified. My lab is studying the interaction of genomes, chromosomes and DNA sequences in polyploids and hybrids in several plant groups including cereals, petunia, banana and others. My work concentrates on repetitive DNA sequences, both tandemly repeated satellite sequences and dispersed transposable elements, their diversity and evolution, as well as their epigenetics as evidenced by chromatin organisation and methylation. We speculated that it is the biological significance of epigenetic phenomena that have lead to the successful evolutionary history of polyploidy and hybrid plant species.

In a recent European collaboration ((PARADIGM) we have studied genomic integration of pararetroviruses that are a recently discovered repetitive sequences class in plants and in petunia and tomato form a significant part of the genome. They possibly show a much wider distribution in plant genomes, but are often degenerate and rearranged. We have recent evidence for pararetrovirus elements in sugar beet and other angiosperms and are in the process of sequencing full elements. Pararetroviruses are closely related to pseudoviridae retroelements and are often found in their physical proximity. Pararetrovirus activation is linked to disease outbreaks and patterns of DNA and chromatin methylation and possibly epigenetic silencing mechanisms. Activation of integrated, but dormant pararetroviruses can be caused by the introduction of wide hybridization and can lead to disease outbreaks through tissue culture or environmental stresses as has been shown for banana.

In wheat and related species, we have found differences in cytosine methylation patterns at symmetrical and asymmetrical sites in the tandemly repeated 120bp repeat DNA family in diploid and polyploid genomes and we are currently investigating whether other repetitive DNA families show similar changes. On the chromosomal level, diploid species of rye and wheat show uniform methylation patterns while allopolyploids have more unevenly distributed methylation indicating de novo methylation and demethylation mechanisms when genomes are combined in polyploid and hybrid species. In wheat breeding lines, incorporating alien chromatin segments important to understand such epigenetic changes both at the DNA sequence level and the global chromatin level to predict the successful

Our studies in banana have looked at retroelements and tandemly repeated DNA sequences, and their genomic flanking sequences were studied showing differential expression, DNA and histone methylation. The close chromosomal proximity and insertion within each other postulates a possible link in the evolution of LTR-retrotransposons, tandem repeats and 5S rRNA genes, but also a role of retrotransposon sequences in gene regulation. This is supported by variable DNA methylation patterns and the presence of repeat transcripts.

Root tip metaphase of rye, Secale cereal ‘Petkus Sping’ (2n=14) after immunostaining with anti-methyl cytosine antibodies (green fluorescence)and fluorescent in situ hybridization with the 120bp repeat DNA probe (red fluorescence). The 120bp repeat family is located in the large subtelomeric heterochromatic blocks that lack DNA methylation while the euchromatin and small intercalary 120bp repeat sites are uniformly methylated. Schwarzacher and Contento have shown that this uniform methylation pattern gets disturbed in hybrid and polyploid triticale.

Page updated 24 November 2008

Completed projects include:

Early events of meiosis

I have used molecular cytogenetic methods to analyse chromosome behaviour during early events of meiosis in Triticeae cereals. I have found that homologous chromosomes first associate at the interphase before meiotic prophase and have postulated a three stage model of homologous chromosome pairing in Triticeae cereals (with relatively large genome size) that involves cognition, alignment and then synapsis. The differential condensation of pachytene chromosomes and the non-random distribution of chiasmata, that I have shown in cereal chromosomes, have major implications for genome organisation, sequence distribution and amplification, chromosome behaviour and possibly gene expression

Evolution of terminal regions of chromosomes

I have studied the long range organisation and possible modes of evolution of repeated sequence families at the telomeres of rye chromosomes, and located microsatellite motifs on metaphase chromosomes in situ. Various motifs show a rich, chromosome-specific and conserved diagnostic banding pattern in rye and wheat. We have found microsatellite repeats occur mainly in the chromatin loops formed at meiotic prophase, in contrast to the subtelomeric satellite sequence families that are closely associated with the synaptonemal complex. Using flow cytometry and sorting of chromosomes, I have found that plant genomes show a remarkable uniformity of AT:GC ratios of all chromosomes, indicative of strong homogenisation events that are different to that found in mammalian genomes.  I located the telomeric repeat (TTTAGGG)n on cereal metaphase chromosomes, and showed that different chromosomes carry different amounts of telomeric repeats at their physical ends; I was able to describe unambiguously for the first time the dispersed distribution of retrotransposon-like elements in plants.

Genomic in situ hybridization

In situ hybridisation using total genomic DNA as a probe, developed by me, has enabled us to identify and localise chromosomes and chromosome segments in cereal plants that include DNA from different species. The technique, now applied world-wide by many research labs, has proven to be valuable for studying the architecture of the nucleus and for following alien gene transfer. We have shown that the nucleus is non-randomly organised, that individual chromosomes occupy tightly defined domains at interphase and that the parental genomes in interspecific and intergeneric hybrids remain separated throughout the cell cycle. We speculate that there are mechanisms for organising the interphase nucleus and that this organisation affects chromosome behaviour during gene expression, chromosome elimination, and during somatic and meiotic division.

Meiotic Gene Analysis

I have isolated, cloned and sequenced the meiotic recombination specific gene DMC1 (disrupted meiotic c-DNA, homolgous to RAD51) in barley (in collaboration with Victor Klimyuk and Jonathan Jones, Sainsbury Laboratory, John Innes Centre). We used sequence homology from the Arabidopsis gene and primers to the conserved region to isolate a 11kb lambda genomic clone and have sequenced most of the gene including the promoter. We have transformed barley to study the activity and specificity of the DMC1 promoter. Foci with antibodies to Rad51 localise near telomeres of rye chromosomes indicating that early recombination events are unevenly distributed along chromosomes and reflect chiasma distribution.

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