Wilhelm bernhard workshop on the cell nucleus

CORRELATION BETWEEN GENE POSITIONING AND GENE EXPRESSION

Philimonenko A. A.¹, Janáček J. ², Weipoltshammer K.³, Schöfer C.³, and Hozák P.<sup>1

1</sup>Institute of Experimental Medicine and ²Department of Biomathematics, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; ³Institute for Histology and Embryology, University of Vienna, Austria
We have investigated the spatial relationship of transcriptionally active or inactive genes within chromosome territories in the interphase nucleus of human fibroblasts. As a model we used paternally imprinted genes located within the 15q11-q13 region of chromosome 15 (SNRPN locus), deletion of which leads to Prader-Willi syndrome. For the simultaneous detection of genes and chromosome territories, we used in situ hybridization with commercially available DNA probes to SNRPN locus, and to the q arm of human chromosome 15. A computer program was written which allows the detection of the border of chromosome territory, and the distance between the border and the center of mass (labelling) of the gene. The analysis demonstrated no significant differences in distances from gene to chromosome territory border between active and inactive genes. Significant portion of genes were found located outside of 15q territory – however, only if the allele were transcriptionally active. In agreement with previously obtained data, we also observed a distinct substructure in interphase chromosome territories. Strongly labeled chromosomal subdomains were surrounded by less intensely labeled areas. Using a tresholding of digital images of human fibroblast nuclei we discriminated these sub-chromosomal domains and evaluated the distances between their borders and SNRPN loci. The SNRPN gene loci were located preferentially at the borders of chromosomal subdomains. These data support the idea that genes are preferentially located at the outer side of domains with condensed chromatin, but no strict correlation was found between active and inactive genes within the entire chromosomal domain. The only striking difference was the presence of ~ 7% of active genes at relatively large distances from the chromosomal territories.