Improving the specificity and throughput of automated analysis of chromatin fine structure in eukaryotic cells

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The molecular mechanism of gene expression is not fully understood, but the rules are the same for all organisms. One important discovery regards the role of chromatin. Chromatin is the name for the proteins compacting the one-meter long DNA molecule so that it fits into the cell nucleus. Active genes possess areas of reduced compaction. There are protein complexes pushing chromatin aside or modify it, so that genes can 'go to work'. The details of these processes are complicated and there are still many open questions. Therefore the chromatin structure of many genes needs to be studied so we can reach conclusions about general principles of the role of chromatin in gene expression, and how chromatin responds to signals coming from outside the cells. However, genes are very large and comprise many thousand and sometimes millions of base pairs and our current methods are too slow. We therefore urgently need methods that speed up the analysis of genes. We have developed a method that allows the rapid examination of the chromatin fine structure of entire gene loci, using a robot. However, although this has greatly improved our capacity to analyze genes, there is still a lot of room for improvement. This proposal aims at doing just that: we propose to further simplify existing technology and to make our assays more specific.