YoussefAyachii / HiCDataAnalysis

Using chromatin-chromatin interaction scores generated by the Capture Hi-C technology, I developed this R code during my six week internship in the Spicuglia lab, part of the INSERM institute (TAGC) related to the Aix-Marseille University, France, in order to identify the DNA interactions happening between different regions, specifically the interaction of the OAS3 Epromoter with its target promoters OAS1 and OAS2, before and after IFN alpha stress stimulation and then to figure out the changes of the 3D chromatin organization upon this stress stimulation.

Scope

Study of the 3D chromatin organization in the context of OAS3 Epromoter regulation inside the OAS cluster upon IFNα stress stimulation

Inside the nucleus of the mammalian cells, the chromatin organization in the 3D space is controlled by intra-chromatin interactions and this special arrangement of the genome plays a crucial role in gene regulation.

To study those interactions and to understand more the 3D organization of the chromatin inside the nucleus, several techniques have been developed, especially the Chromosome Conformation Capture (3C) and 3C-derived methods.

Here, we focus on the study of the chromatin interactions happening inside and nearby the OAS cluster of the human chromosome 12 which comprises the OAS1, OAS2 and OAS3 genes.

These three genes are known to be activated after a Type-I Interferon-alpha (IFNα) stress response and this cluster is known for its OAS3 Epromoter which, once activated, has an enhancer activity on the OAS1 and the OAS2 gene promoters.

Here, we use a 3C based technique, Hybrid Capture Hi-C, to comprehensively detect the OAS3 Epromoter interactions with its target OAS1 and OAS2 gene promoters before and after IFNα stress stimulation and to quantify the intra-chromatin interactions happening inside and nearby the OAS gene cluster upon the IFNα stress stimulation.