Mention “mutated DNA” to non-scientists and they’ll think of something harmful, genetic errors to be avoided at all costs. Mention “mutated DNA” to geneticists, and the reaction may be quite different, especially since the advent of CRISPR. This new genome-editing tool lets researchers modify the base sequence of DNA at very precise locations – essentially, producing tailor-made mutations – even in living organisms! Michaela Willi and her colleagues, for example, use CRISPR to generate mice with mutations in a super-enhancer that controls activity of a gene in mammary gland cells.
What brought from her home in Innsbruck to a high-powered research lab at the National Institutes of Health (NIH)? After an initial focus on Bioinformatics, she “started to see a connection between [her] study and the research for clinical applications.” Genomics research “was completely new for me,” says Willi, but “I realized soon how much I enjoy … bridging the two disciplines Biology and Bioinformatics to understand mechanisms of gene regulation.”
So, back to that super-enhancer… As cells differentiate they change their function, their genes becoming more or less active. These changes in gene activity are controlled by long sections of DNA called super-enhancers, which can boost gene activity up to several-thousand times! And what turns the super-enhancers on? Transcription factors, which can respond to levels of hormones or cytokines, bind to super-enhancers “in dense clusters” to turn them on.
One particular transcription factor, a protein called STAT5, regulates mammary gland activity under the influence of pregnancy hormones by shaping the super-enhancers’ activity. STAT5 exerts major control in mammary tissue, affecting several hundred super-enhancers. Willi and co-first authors Ha Youn Shin and Kyung Hyun Yoo, along with other team members, studied a mouse mammary gland super-enhancer made of three modules, which shapes Wap gene activity.
“Whey acidic protein” is the major whey protein in rodents’ milk, so the Wap gene is important to milk content. Using CRISPR to alter DNA in ways that disrupt the binding of STAT5 to the super-enhancer’s three modules (individually and in combination),thegroup discovered – for the first time ever – that the modules play different roles, a sort of hierarchy! STAT5 binding to the first two modules has little effect, but binding the third module causes 90% of the increase in gene activity. Only when all three modules are impaired does the super-enhancer totally lose function. Even more complex, the first module can bind transcription factors other than STAT5. Disrupting the binding of all these factors “silences” the whole super-enhancer, so modules two and three never become functional. Thus, the first module “launches” the whole super-enhancer!
The study by Ha Youn Shin, Michaela Willi, and Kyung Hyun Yoo reveals a lot, not only about the Wap gene, but about super-enhancers in general. Their work will contribute to biology per se, and also to fields like clinical medicine, as “a more complete understanding of biology will allow a better understanding of, for instance, cancer.” Despite noting wryly that “the more insights I get, the less I think I know,” Willi is excited that a combination of genomics and bioinformatics can open doors to solving new and emerging challenges. To a researcher for whom “Curiosity is a driving force!” this field is the perfect place to be.
The preceding article is part of a series featuring the scientific work of 20 young Austrian researchers, all who are active members of the OSTA's Research and Innovation Network Austria. The initial presentation of their work took place at the ASCINA poster session under the auspices of the "Austrian Research and Innovation Talk" in Toronto on October 21, 2016. Three of these scientists were subsequently awarded the ASCINA award the same evening, honoring their outstanding scientific work.