The regulatory effect of 3D chromatin organization on genes resistant to reprogramming

To understand how cells in our body resist changes in gene expression would be instrumental for better understanding the causes of diseases and designing improved treatments. We have recently identified a possible link between resistance to transcriptional reprogramming and 3D chromatin organization. We hypothesize that genes with low resistance to transcriptional reprogramming occupy accessible 3D positions in the nucleus, while more resistant genes are embedded within more topologically restricted chromatin. However, further studies are needed to elucidate the role of 3D genome organization in the stability of gene silencing and resistance to transcriptional activation. We will use Hi-C, a method allowing the analysis of the spatial organization of chromatin, to define the relationship between the resistance to transcriptional reprogramming and genome organization. We will then study dynamic changes in chromatin topology during induced pluripotent stem cell reprogramming using single-cell Hi-C. This will reveal the relationship between the kinetics of chromatin domain formation and the timing of transcriptional activation. Furthermore, we will identify how modulating chromatin organization affects the resistance to transcriptional reprogramming using genome editing coupled with transcriptomic approaches. Altogether, we aim to better understand the effects of chromatin organization on gene expression, and ultimately gene regulation, cellular identity and diseases.