Research Report 2003 - Max-Planck-Institut für molekulare Genetik

Department of Vertebrate Genomics
8
Analysis of genomic sequences
Mapping and sequencing projects
A major effort during the last 6 years has been directed at mapping of chromosomes
(Yaspo, Sudbrak) and entire genomes (Himmelbauer, Schalkwyk*, Knoblauch*), and
the determination of genomic sequences, culminating in the completion of the sequence
of chromosome 21 (Yaspo, Reinhardt), the working draft of the human genome and
finally the recent publication of the essentially completed genome sequence. Since
then, we have increasingly focused on the use of genomic sequencing to understand
the evolution of regions of the human genome (Yaspo, Sudbrak, Reinhardt). In one of
these projects, the sequencing of chimp chromosome 22, the equivalent of human
chromosome 21, has been completed in collaboration with groups in Germany, Japan,
China, Taiwan and South Korea. The results, currently being prepared for publication,
provide fascinating insights into the biological differences between man and our closest
relative. The sequence of the rat MHC has been completed, and submitted for
publication (Himmelbauer, Reinhardt). To try to understand more distant evolutionary
processes, we have continued to work on the genomic sequence of Oikopleura, a chordate
with an exceptionally small genome (app. 70 Mb). In a first whole genome shotgun
phase, a coverage of approximately 1.1 x has been achieved. To minimize the
effect of the high polymorphism rate, we have now shifted to BAC based sequencing,
with the progress limited by lack of funding (Reinhardt, Yaspo).
Genetic analysis
Genotype-phenotype correlations in man will increasingly require the application of
more effective genotyping tools. For this, new protocols for SNP genotyping (Gut*,
Sauer) and microsequencing (Nordhoff*) based on mass spectroscopy have been developed.
An alternative optical approach for SNP typing is currently under development
(Soldatov). New approaches to compare the sequences of candidate genes in
patients and controls, and to analyze their haplotypes have been developed and are
being applied in a number of different disease areas (Hoehe, Reinhardt).
Analysis of transcripts
Further insights into evolutionary processes in key organisms with larger genomes
have been derived from the analysis of transcripts, based on a combination of the
oligonucleotide fingerprinting approach to assign cDNA clones to clusters corresponding
to different genes, combined with a limited amount of cDNA sequencing. This
approach has been applied to a number of different organisms, e.g. zebrafish (Clark*),
different plants (Radeloff*), man and mouse (Radeloff*, Janitz), cow (Janitz) etc.
Among other projects, this has given insights into the set of genes available to amphioxus,
a cephalochordate, and sea urchin, an echinoderm, representing key stages in
deuterostome evolution. This work has contributed to understanding the evolution of
the vertebrate genome, and especially the ‘Ohno hypothesis’, according to which two
whole genome duplications of a chordate genome have led to the vertebrate genome
(Panopoulou, Poustka).
Functional Genomics
Analysis of gene expression
Efficient, sensitive techniques to detect and quantify patterns of transcription have
been a major focus in functional genomics. Starting from our first arrayer developed
by us in 1987, we have carried out long term technology development in this area,
from the first filter based complex cDNA hybridization screens to high throughput
chip hybridization systems (Eickhoff*, Hultschig), and applied these techniques to a
number of biological (and medical) problems (Yaspo, Nietfeld, Ruiz, Sperling, Soldatov
etc.). A number of global (ENSEMBL chip by Yaspo, RZPD) and disease specific
(Ruiz, Sperling, Hultschig) chips have been constructed.
* former member of the department