UKRI/BBSRC-NSF/BIO Building synthetic regulatory units to understand the complexity of mammalian gene expression

The synthetic cells of the future will be produced for a multitude of end uses, including agriculture, biotechnology and production of biomaterials. These synthetic cells would perform best if researchers could turn specific genes on and off at will, and precisely tune the level at which these genes are expressed. Central to this goal is a deep understanding of how regulatory elements in the DNA control the timing and level that genes are expressed.

The long-term goals of this project are to better define the functions of different DNA regulatory elements, to determine how these elements work together to control genes, and to use this knowledge to engineer mammalian cells that precisely and controllably express a desired set of genes. This project will be complemented by an innovative program, the yeast art program, that will be developed as a major outreach tool to help the public better understand the goals and potential of gene engineering.

Recent work has greatly increased our understanding of enhancers - one of three fundamental genomic elements that orchestrate gene regulation. With promoters and insulators, they form detectable and dynamic 3-D structures that drive precise spatiotemporal programs of gene expression. The alpha-globin locus offers a well-established and tractable model of a mammalian regulatory domain, whereas other loci are not as easily defined and manipulated.

Powered by recent advances in de novo DNA design and synthesis approaches, together with the new genomic engineering and analysis strategies, multiple versions of the entire mouse alpha-globin regulatory domain have been generated and used to identify novel genomic elements called ‘facilitators’. These enhancer-like elements have no inherent activation potential but play crucial roles in modulating the activity of canonical enhancers.

Enlightened by this experience, this project aims to address key questions in the gene expression field by initially creating and analyzing 11 new hypothesis-driven mouse genetic models based on the natural endogenous alpha-globin regulatory landscape. Further alleles will be designed depending on the results obtained from these initial constructs. Understanding the rules underlying the communication and relay of information between the main classes of cis-regulatory elements will transform our understanding of the code for life, with the ultimate goal of synthesizing minimal fully-functional mammalian alleles and genomes.

This collaborative US/UK project is supported by the US National Science Foundation (NSF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC), where NSF funds the US investigator and BBSRC funds the partners in the UK.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.