In his Masterclass, keynote speaker Eddy Rubin (Director of the DoE Joint Genomics Institute, Walnut Creek, USA) showed that he’s a big fan of massive comparative experiments. Such sequence-based experiments may seem noncommittal − just compare the whole bunch and see what comes up − but they can yield fascinating insights.

Conserved regions

For example on extremely conserved non-coding regions in the genome. Such regions are usually associated with important functions, including as enhancer sequences. To find tissue-specific enhancers, Rubin applied distant comparisons to select extremely conserved elements. Testing these elements for tissue-specific enhancer activity was done using constructs in mouse embryos. Of 500 extremely conserved elements, 230 tested positive on enhancer activity. These enhancers apparently stimulate expression early during embryogenesis and most are linked to neural development.

Additive pattern

Pursuing the functions of tissue specific enhancers a bit more, the team studied the interaction between enhancers. Interestingly, they exhibit an additive pattern. If enhancer A stimulates expression in limb and enhancer B in forebrain, then putting the two together simply leads to an addition; expression is shown in both limb and forebrain. No signs of interference are seen, which underlines the modular nature of enhancers. As gene regulation is widely seen as the motor of evolution, studying enhancer biology may generate a possible mechanism for the evolution of complex expression patterns.

Human or chimp

Studying non-coding conserved elements also sheds light on a long-standing question that intrigues scientists and non-scientists alike: What makes us human? Searching for highly conserved elements that show specific changes in humans led to an 81 base pair enhancer element that contains 13 human-specific substitutions. To establish whether these substitutions account for the specific human expression pattern, a ‘humanized’ chimp construct was prepared that indeed showed the human expression pattern. In turn, the ‘chimpanized’ human construct exhibit the chimp expression pattern. According to Rubin, the 13 bp substitutions seem to define ‘human’ or ‘chimp’.

Revealing answer

When asked by a participant whether they studied the effect of singular substitutions also to find out whether a gradient in expression alteration is shown, Rubin’s answer was revealing. “We didn’t study that, life’s short. Shoot at the goal while you have a chance.” Perform massive sequence-based functional experiments that don’t require a lot of biology and who knows what you’ll find, that’s the Rubin approach.

[Esther Thole]