Periodic Reporting for period 3 - Gen-Epix (Genetic Determinants of the Epigenome)
Reporting period: 2019-06-01 to 2020-11-30
SALL4 is of wider interest for several reasons:
• It is mutated in a human skeletal disorder (Okihiro syndrome)
• It is an essential inhibitor of differentiation that safe-guards pluripotency of stem cells
• It is over-expressed in many cancers and is a potential target for anti-cancer therapeutics
We hypothesized that proteins could in theory read base composition by binding to strings of homogeneous A/T sequence, thereby amplifying the relatively subtle differences between domains. We screened for such proteins and identified SALL4, a protein that is expressed in pluripotent stem cells and implicated in a variety of cancers. Loss of SALL4 is long known to cause precocious ESC differentiation, but the underlying mechanism is unknown. We have found that discrete inactivation of the AT-binding zinc finger cluster causes up-regulation of AT-rich genes involved in neuronal differentiation and mimics the severe phenotypes of cells and mice that completely lack SALL4. These results strongly suggest that recognition of AT motifs is at the heart of SALL4 function.
Our studies so far offer a compelling explanation for SALL4 function. They indicate that the base compositional environment of a gene is sampled by SALL4 via the frequency of its A/T recognition motif, resulting in enhanced gene repression where the motif is most abundant. This “blanket” silencing mechanism stabilises the pluripotent state by preventing inappropriate expression of differentiation genes.
More broadly, by showing that the DNA sequence environment of a gene regulates its expression, we provide the first mechanistic evidence that base compositional domains are not merely a biologically irrelevant by-product of genome evolution, but confer a positive selective advantage to the organism.
We suggest that the evolutionary, developmental and disease implications of our future work will uncover parallel mechanisms of wide importance.