Abstract

The eukaryotic genome is extensively folded to fit in the small volume of the cell nucleus. Several lines of evidence have suggested a functional relationship between the structural folding of chromosomes and gene expression; however methods to systematically analyze chromosome folding were missing. This thesis describes the development and application of a novel method, chromosome conformation capture on chip (4C). In 4C one genomic fragment is selected (e.g. a gene promoter), and for this viewpoint fragment all the DNA that is found in spatial proximity is captured and analyzed. We applied 4C to analyze the nuclear surroundings of the beta globin locus in two tissues, one in which the locus is active and one in which it is silent. We found that the beta globin locus contacts other active parts of the genome when it is active and silent genomic regions in the tissue in which it is not expressed. A second application of 4C is the detection of genomic rearrangements. Any given fragment in the genome will always be surrounded by the parts of the genome that flank it on the linear genome map, therefore these sequences will always appear most strongly in the 4C data. This allows the identification of new genomic neighbors in case of a rearrangement.4C uniquely allows the detection of genomic breakpoints rapidly and at high resolution. To optimize the technique further, 4C was adapted from a microarray based to a sequencing based method.

F.G. Grosveld (Frank)
Erasmus University Rotterdam
The work presented in this thesis was performed at the department of Cell Biology at the Erasmus MC in Rotterdam.
hdl.handle.net/1765/77016
Erasmus MC: University Medical Center Rotterdam

Simonis, M. (2008, December 17). Chromosome Conformation Capture on Chip (4C): Meeting genomic neighbors. Retrieved from http://hdl.handle.net/1765/77016