New model for long-range chromatin reorganisation upon enhancer-driven gene activation
Benabdallah, Suzanne Nezha
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Enhancers are non-coding DNA sequences which are able to activate the expression of a gene in a specific tissue manner and at a precise stage during embryonic development. First identified almost 40 years ago, our growing understanding of enhancers has transformed the concept of gene regulation to recognise the key role of these sequences in the expression of many genes. Moreover, the identification of human diseases caused by genetic variation in non-coding enhancer elements highlights the importance of characterising enhancers in order to understand human disease. However, enhancers are often located far from the promoter they influence and the mechanisms through which enhancers govern gene expression remain unclear. The most widely accepted model for the action of distal enhancers involves the formation of a chromatin loop, in which the enhancer and promoter physically interact at the loop base. The kinetics or molecular basis for the formation of enhancer/promoter loops is unknown and it remains unclear whether this mechanism of enhancer communication is universal, or indeed whether it is the most pervasive. The aim of my PhD is to investigate further the mechanism of action of distal enhancers in the regulation of developmental genes. Using chromatin profiling during the differentiation of embryonic stem cells to neural progenitor cells in order to see which Shh enhancer is active in neural progenitor cells (NPCs), I report the identification of a novel long-range enhancer for Shh - Shh-Brain- Enhancer-6 (SBE6) – that is located 100kb upstream of Shh and that is required for the proper induction of Shh expression during a neural differentiation programme. SBE6 enhances Shh expression during the differentiation of neural progenitor cells (NPCs) and is active in the brain of developing zebrafish and mouse embryos. Next, using a super-resolution 3D-FISH based approach to study the enhancer-driven activation of the Sonic hedgehog gene (Shh) I have identified a novel mechanism of longrange enhancer regulation that is incompatible with the looping model. Instead, gene activation is associated with an increase in nuclear distance between Shh and Shh-Brain- Enhancers. Using a synthetic biology approach I have determined that the chromatin unfolding is regulated specifically by the Shh-Brain-Enhancer and is mediated by the recruitment of transcription factor SIX3 and Poly (ADP-Ribose) Polymerase 1. Chromatin decondensation upon gene activation has been observed previously in Drosophila polytene chromosomes. I suggest an analogous decompaction is driven by Shh-Brain-Enhancer to promote the activation of Shh in mouse neural progenitor cells. This ‘chromatin unfolding’ model represents a new mechanism of long-range enhancer-promoter communication in addition to the looping and tracking models.