Jonathan Henninger runs a laboratory at Carnegie Mellon University, in Pittsburgh, PA, USA. His lab explores how RNA molecules regulate gene expression at multiple scales in health and disease.

Can you tell me a little bit about your background and where you are now?

Yeah, absolutely. I did my undergraduate degree in my hometown, at the Indiana University of Pennsylvania, where I studied biochemistry. I really love the idea of applying chemical principles to biology.

I did my PhD at Harvard, where I became fascinated by stem cell biology and gene regulation. Understanding how a single cell can develop into a multicellular organism was super fascinating to me. I worked on tracking individual clones of blood stem cells through development into adulthood in zebrafish.

To really understand how these cells were misbehaving, you had to understand very fundamental gene regulatory mechanisms, and so I joined a gene regulatory group at MIT after that. This was right at the time when we realised that biomolecules in our cells — proteins, DNA, RNA — all join together to form higher-order compartments called biomolecular condensates, and I worked on the RNA side of things.

A couple of years ago, I started my own group at Carnegie Mellon University in Pittsburgh, and we’re very much excited by studying what makes condensates form and what regulates them.

Is there any reason why you became interested in RNAs specifically?

Because there was a lot of mystery there. It had been recognised since the early- into the mid-2000s that a bunch of gene-regulatory elements were transcribed into RNA. Over time, more and more evidence accumulated that at least some of these types of RNAs were functional, but we didn’t really know what they were doing. We soon realised they may be affecting condensate formation.

Would you say there are any big challenges to working with RNA?

Tons. RNA is more unstable [than DNA]; it forms very unique and dynamic structures, where as DNA is a bit more constrained. Some RNAs have very short half-lives – some can last for days in the cell, but some only last a few minutes.

We have things like AlphaFold which can predict protein structure, but this doesn’t really exist for RNA, as it doesn’t have a single particular structure it likes to form.

There also aren’t really tons of tools out for specifically manipulating RNA reproducibly and stably – any time you try to perturb RNA synthesis, you’re also perturbing a whole bunch of other chemistries within the cell.

You recently had a paper out about transcriptional condensates, and how RNA helps them to form. Can you tell me a bit about what you found?

This was a really fun collaboration! We were investigating what actually contributes to the patterning of condensates. When we say patterning, we mean the size of each condensate, the number of them that exist, the spacing between them.

In the nucleolus [region of the nucleus where ribosomes are formed], we had an inkling from decades of research that ribosomal RNA transcription may play a part, and we saw that disabling this with inhibitors made condensates join up.

We realised that having condensates spread out is a lot more efficient for the cell to transcribe RNA and stop unprocessed ribosomal RNA from building up, which can be toxic.

When we deliberately changed the way the condensates are organised, it didn’t impact transcription itself much, but it did dramatically stop the cell from processing the RNA as easily. This is all vital for the inner workings of the cell.

What do you think the next step is for this research?

There’s lots of fun routes to consider! There are disease-associated mutations that impact how some condensates form, and I think this will lead to a whole new field that change how we think about some disease mechanisms.

I also want to look at transcriptional condensates at RNA polymerase II-driven genes – these contribute to whether a cell becomes a blood cell, liver cell, brain cell, and so on. This could be a whole new layer of epigenetic regulation, which is pretty cool.

What advice would you give to younger people thinking about working in science in general?

Don’t downplay the effect of curiosity. [In scientific research] 99% of what you do is going to fail. Getting comfortable with that is a major hurdle: arre you willing to put in the effort to try to figure it out, rather than have someone else tell you how things should go? Developing that independence and that curiosity is very important.

I would also be conscious of LLM use – although they are useful in some places, AI tools should not replace scientific thinking.

What do you do to enjoy yourself outside of work?

We have a new baby, so he takes up a lot of my time now! It’s a huge joy. During the pandemic, I also got really into chess. And, like a lot of other people, I love to read.

Cool! I’ve started playing also (against a computer) — I enjoy it, but it’s definitely tough sometimes…

It is. I think I’ve played over, like, 15,000 games now. When you do 1 minute games they rack up pretty quickly, and you slowly improve!

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