Collective interactions dominate gene regulation in eukaryotes

‘What is true for E. coli is true for the elephant’, Nobel laureate Jacques Monod wrote in 1954. It seems now that the appropriate response might be that famously offered, in lieu of contradiction, by an obsequious newspaper editor to his proprietor in Evelyn Waugh’s satire Scoop: ‘Up to a point, Lord Copper.’ Monod won his Nobel with François Jacob for elucidating the molecular mechanism of gene regulation – how transcription of genes is turned on and off – in E. coli. And for sure, gene regulation happens in elephants too. But the molecular principles governing this process in complex eukaryotes like elephants and us turn out to be rather different to those for bacteria. 

Gene regulation is arguably the central process of living things. In every cell at every moment, the transcription of genes is being turned up or down. In bacteria, evolution seems to have come up with a clear and logical way of doing this. Proteins called transcription factors (TFs), with parts shaped to recognise and bind to specific DNA sequences called promoters, trigger the production of mRNA from the respective gene by the RNA polymerase enzyme: the process of transcription. 

It was long assumed that gene regulation in eukaryotes followed much the same rules, albeit perhaps with more components that assemble into some sort of stoichiometric molecular machine. But over the past two decades or so it has become clear that this isn’t so. How our own TFs work seems to get more baffling the closer we look at it. 

Less specific, more sites

For one thing, eukaryotic TFs seem to be less specific than prokaryotic ones. There are potential binding sites for them all over the genome, but only a small proportion of these are occupied. The same TF might bind to different sites in different cell types,¹ and two TFs that seem to have the same preferences for a given DNA motif might bind in different places. Some TFs seem to bind to DNA where there’s no recognised binding motif at all. And depleting a given TF might alter gene expression even when there’s no detectable binding.² What’s going on?

 There’s a clue in the nature of eukaryotic TFs themselves. They typically contain so-called intrinsically disordered regions (IDRs), where the polypeptide chain does not adopt a well-ordered fold but remains rather loose and flexible. These IDRs enable the protein to bind to a variety of partners via many weak interactions. What’s more, these TFs don’t generally work on their own, but in pairs or small groups, and the specificity they show for regulating genes seems to be a combinatorial, collective property. 

Figuring out the rules behind all of this is hard not just because they seem so counter-intuitive but also because the experimental methods are limited. How do we know, say, where a given TF binds? Existing techniques might not reflect what really goes on in normal cells, for example because they just don’t work in vivo. Robert Tjian of the University of California at Berkeley, US, and his colleagues have reported a new method that overcomes some of these problems, using fluorescent ‘sender’ and ‘receiver’ dyes that can be attached to proteins and which light up when they are close together.³ The method reveals fleeting interactions between proteins that would be invisible to previous techniques. 

Beyond DNA binding domains

The researchers found some puzzling results for a human TF called Sp1, which regulates various genes in different cell types. Although it has a DNA binding domain (DBD), that domain alone, when separated from Sp1’s IDRs, doesn’t show up in the places where Sp1 itself does. In other words, binding specificity isn’t all about the DBD. 

Perhaps weirder still, Sp1 can be given a completely different DBD and still show up at the same sites as the native form: the DBD, previously considered the key determinant of binding specificity, is shockingly interchangeable. It seems that the IDRs of the protein matter more for its targeting. Taken together, the results suggest that the specificity of eukaryotic TF binding is underspecified in the proteins themselves, being instead an emergent and collective phenomenon. 

Why do things this complicated way when there was a perfectly good bacterial option available? One possibility is that it creates the context-dependence of regulation that higher organisms need. Perhaps, the researchers suspect, the cell nucleus is not just a compartment for housing the genome but also a place for convening these largely unstructured molecular conversations out of which decisions about gene regulation emerge. 

In any event, Tjian tells me that the findings show the pitfalls of ‘reducing an organic system to machine-like parts and assuming that specificity is intrinsic to those parts.’ Only by developing a technique ‘that allowed us to eavesdrop on the conversations between unstructured proteins in their true native context’ could they see beyond that paradigm.