Biology never makes things easy for us.

It’s tempting to think of the genome as a well-oiled machine, with separate regions that join neatly together like Lego bricks to perform an overall function. However, over recent years, it’s become clear that this “one region = one function” rule is not quite the case.

This is especially relevant for regulatory sequences, which are involved in ensuring genes are expressed, or “switched on”, at the right time and at the appropriate level for the cell’s requirements, and are absolutely critical for cell function.

The most well-studied regulatory elements are promoters and enhancers. Promoters are found just before a gene sequence, and are the start line from where transcription begins. Enhancers are sequences that can help turn this transcription of a gene up or down, even if it’s miles away, like a dimmer switch.

We now know that some regions of DNA can act as both a promoter and enhancer at the same time, but there’s never been a way of measuring this directly.

Haiyuan Yu’s team at Cornell University in New York, USA has developed a method to determine the identity of regulatory elements in one shot to see whether they act more like enhancers or promoters.

They call this the Quantitative Unifying Assay for Simultaneously Active Regulatory Regions by sequencing (QUASARR-seq) (I love scientists’ ability to make acronyms that work, by the way, because how long did they take to come up with this?!).

The system

Let’s say you’ve found a hypothetical sequence, called TCD, and wanted to determine how it worked with QUASARR-seq. How exactly does this work?

Sequence TCD would be inserted into cells with two sequences either side of it, called barcodes. One spits out signals saying “TCD is being used as a promoter”, and the other signals that “TCD is being used as an enhancer”.

These signals are then quantified with a sequencing machine to determine the identity of sequence TCD and how it’s acting at any given moment.

Two peas in a pod

The authors looked at hundreds of sequences simultaneously with QUASARR-seq, and found that a vast majority — 96.3% — of the sequences that acted as enhancers also had promoter activity. This suggested that the activity of both was highly, though not entirely, intertwined.

Moreover, promoter and enhancer activity were positively correlated; the more a sequence behaved like one, the more it behaved like the other too. This is called a “positive feedback loop” — imagine you sleep less, so you drink more coffee, which means you sleep less… et cetera. The authors believe this positive feedback may be due to promoters and enhancers making use of the same proteins nearby in the nucleus, such as activating transcription factors.

The authors also tested whether they could validate their new method by artificially activating a promoter to see if its enhancer activity increased. To do this, they used CRISPR activation (CRISPRa), which essentially shuttles a load of activating proteins to a specific genomic region to switch it on. Sure enough, artificial promoter activation with CRISPRa made them act more like enhancers at the same time.

Implications beyond “regulatory logic”

This research is clearly important for decoding the underlying set of rules behind how our regulatory sequences in our cells act. But does it have implications beyond that? Absolutely.

In some diseases, there are genetic variants that stop promoters from working properly, wreaking havoc on gene expression. The authors wanted to test whether these variants impacted enhancer function too.

In this case, they investigated a promoter called APC, known to be mutated — i.e., the genetic sequence altered — in some gastric cancers. QUASARR-seq revealed that mutating the APC promoter in the same way found in gastric cancer patients also impaired APC‘s ability to act as an enhancer.

“Yeah, and?”

This final finding may change the way we think about targeting regulatory sequences when treating diseases. If you wanted to make a drug to block the APC promoter’s activity somehow, you would have to think about how its reduced enhancer activity could impact the cell’s function, and any treatment approach would have to consider this to avoid causing genomic chaos. In future, clinical researchers, as well as molecular biologists, may therefore have this paper bookmarked.

Something I think may be interesting for future work with QUASARR-seq may be to change the cell’s environment, such as stressing cells with heat or treating them with drugs, to see whether promoters become more enhancer-like over time, or vice versa, and whether this impacts regulatory networks. Let’s see 🙂

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