Transcription is a fundamental step in gene expression during which soluble protein factors are recruited to the DNA or chromatin template. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation and increasing evidence indicate that gene activation or silencing is often associated with repositioning of a certain locus relative to nuclear compartments and other genomic loci.
We have been focusing our attention on the role of chromatin and higher order chromatin structures in regulation of HIV-1 gene expression. In our recent work we demonstrated that HIV-1 provirus undergoes a peculiar structural change, namely gene loop, while transcribing. Which are the cellular determinants that allow the virus to efficiently form the gene loop structure while transcribing is one of our current interests. Localization of genes to different parts of the nucleus has the potential to promote or inhibit transcription and we are currently soughing to understand the importance of specific molecular interactions between HIV-1 proviral genome and nuclear structures by employing fluorescence in situ hybridization (FISH) and immunofluorescence-FISH (immuno-FISH), chromatin immunoprecipitation (ChIP) and chromosome conformation capture (3C).