Research Projects of Dr Trude Schwarzacher
1. Pararetroviruses and plant genome organization
2. Function of meiotic and recombination specific genes
3. Gene expression and promoter studies
4. Relation of recombination to genome organization
5. Biodiversity and evolution: the application of micro-array technology
6. Virus sequences and host plant genome interactions
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.
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.
I have isolated, cloned and sequenced the meiotic recombination specific gene DMC1 ( d isrupted m eiotic c -DNA, homolgous to RAD 51) 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 DMC 1 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.