Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (RNA-Seq)

Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. This study investigates the cis genetic elements as well as trans elements that drive this process in order to better understand how differentiation rewiring occurs. cHi-C experiments of mouse ESC or NPC wt cells. cHi-C experiments of partial Zfp608 deletion, polyA insertion at the Zfp608 TSS, deletion of element A, deletion of element B, dual deletion of element A and B, deletion of CTCF motif at the element A - all in ESC and NPC cells. cHi-C of mouse ESCs that overexpress Pax6.