What makes for a powerful enhancer sequence?

Posted by Biome on 23rd July 2013 - 1 Comment

How did the zebrafish (pictured below) get its stripes? The stripes are of course a product of the tissue-specific expression of GFP; the ability to control the tissue specificity of gene expression is an innovation that dates back to the rise of multicellularity, and the use of GFP as a reporter is a common method used to determine the tissue specificity of a given gene-regulatory sequence.
Understanding what makes a gene regulatory sequence powerful is useful both for those data crunching large ‘omics’ datasets and for genome engineers who wish to design gene expression patterns.

Tissue specific GFP expression in a zebrafish embryo manipulated using TALENs. Image source: Lim et al, Genome Biology, 2013, 14: R69

In a research article newly published in Genome Biology, Nadav Ahituv, Katherine Pollard and colleagues from the University of California San Francisco, USA screen all possible six base-pair DNA sequences – the approximate size of a transcription factor binding site motif – in zebrafish embryos to find out how different combinations of base pairs drive tissue specificity of gene expression. On the basis of the screen, novel synthetic enhancer sequences for tissue-specific expression are developed.

The new framework for enhancer sequence design that emerges from the study comes at a very interesting time for genome engineering and synthetic biology. A recent flurry of papers have introduced highly targeted cut-and-paste methods for editing genomes in living cells, some of which were recently spotlighted in Genome Biology. Indeed, the zebrafish image shown here is taken from yet another addition to this cannon of methods published in Genome Biology: a whole-locus deletion toolkit that can be used for the excision of a wide variety of genomic elements, including regulatory sequences such as enhancers.

The new array of easy-to-use methods have forced many scientists to ask themselves how we can exploit the new technologies to address important questions. To put it another way, we are entering the discovery stage of genome engineering. But for the full potential of this discovery stage to be met, we need to better understand the sequences that we are editing, and imaginative studies such as Ahituv’s enhancer screen are a perfect starting point for doing so.



A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N et al.
Genome Biology 2013, 14:R72

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  • Genome Biology

    If you find the Genome Biology paper interesting, we highly recommend that you also read the Ahituv lab’s related paper in Nature Genetics http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.2713.html

    Both papers screen libraries of synthetic regulatory sequences, but there are key differences. Whereas the Genome Biology paper looks at enhancer activity of all possible 6bp sequences in different tissues during zebrafish development, the Nature Genetics paper examines 5,000 sequences that were designed based on transcription factor binding site patterns – and does so not in zebrafish embryos but a mammalian hepatic context (in livers extracted from live mice and in the human liver-derived HepG2 cell line).