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Dr. Carol Chen Talks Epigenetics and Bioinformatics

By February 7, 2018October 6th, 2023No Comments

Dr. Carol Chen is a recent doctoral graduate in the laboratory of Dr. Matt Lorincz in the Molecular Epigenetics Group at the University of British Columbia. Dr. Chen is finishing up in the lab, and will be starting a postdoc in the laboratory of Dr. Nada Jabado at McGill University in February. We sat down with Dr. Chen to discuss her research: past, present, and future.

What have you been studying throughout your time as a PhD student?

My PhD project stemmed from this really old observation about a particular histone modification, which is that all eukaryotic cells undergo widespread phosphorylation on serine 10 of histone H3 (H3S10), and that this occurs during mitosis. Paradoxically, previous studies looking at interphase cells discovered that this mark is found within actively transcribed regions of the genome. So there’s this interesting contrast, where H3S10 phosphorylation is found on very condensed, inert chromatin, but is at the same time also associated with active regions. I wanted to characterize this mark in terms of when and where its occurring in mammalian cells.

Did you go into the project with an idea of what might be causing this paradoxical placement of H3S10 phosphorylation in mitotic and interphase cells?

We had some idea that H3S10 phosphorylation may be involved in some crosstalk with an adjacent histone modification, H3K9. This residue is well known to be a silencing mark when methylated. We hypothesized that S10 phosphorylation may act as a means of blocking K9 methylation, thereby preventing the silencing effect of the latter heterochromatic mark. So we set out to prove this in an embryonic stem cell system.

We showed that indeed this was the case. S10 phosphorylation in interphase cells marks broad expansive domains, and when you disrupt it you get accumulation of heterochromatin at previously transcribing genes. What was really interesting was that this relationship goes both ways: if you remove the heterochromatin, the euchromatin also spreads, leading to activation of nearby repetitive elements.

We also looked at this dynamic in differentiated cell types such as fibroblasts. We found that the relationship between removing heterochromatin and having euchromatic spread is still maintained, but that the euchromatin compartments in differentiated cells are much more confined with localized punctate peaks. This has interesting implications as there’s this idea of “hyperdynamic plasticity” associated with stem cells, which allows them to have more accessible chromatin that is more readily able to express certain lineage markers and differentiate into different cell types. Conversely, terminally differentiated cells are more locked into their epigenetic state, so our finding falls nicely in line with that.

To bring it back to original observation, we think H3S10 phosphorylation is functioning to dynamically detach chromatin from the nuclear scaffolding, and in doing so, facilitate access to transcription and replication factories in interphase. This would explain why H3S10 phosphorylation is transiently found on inducible genes before transcription and constitutively mark early-replicating regions. During mitosis, the rest of the genome is phosphorylated then detaches from lamina entirely to condense into chromosomes.

You’ll be starting work on your postdoc in the laboratory of Dr. Nada Jabado at McGill University soon. Will you be continuing in the same area of research?

Yes. Crosstalk between histone modifications is something that really interests me and that I’d like to continue to pursue. For my postdoc I’ll be looking at crosstalk of histone modifications in neural development and glioblastoma progression.

Dr. Nada Jabado’s lab has previously found that 60-70% of pediatric glioblastomas contain a histone H3 variant with a point mutation on H3K27 or G34, which prevents chromatin modifying enzymes from binding these nucleosomes. More specifically, they sequester the histone methyltransferase PRC2, and in doing so recapitulate a loss-of-function mutation in that complex. But the two types of tumours have very distinct clinical pathologies. K27 mutations are localized to the midline of the brain, and are typically more aggressive, whereas G34 mutations are found on the periphery of the brain and linked to better prognosis. G34 mutations also typically present older and are more amenable to treatment. There’s been some suggestion that these two marks hinder one another, so I’d like to characterize them further.

ChIP-Seq and bioinformatics have been central to your research throughout your graduate studies. Do you foresee yourself continuing pursuing these techniques/areas throughout your postdoc?

Yes, but I also want to broaden my horizons. I’ve been interested in mouse work for awhile now, and to study this type of crosstalk regulation you really need to study transgenic mice or knock-out mice. So I’m interested in taking what I know from Chip-seq and expanding that to using primary cells.

As an expert in the field, what advice would you give a researcher thinking about getting into bioinformatics?

Good question! I think bioinformatics is super valuable. If you’re not learning bioinformatics for your own research, you should at least be learning it so that you can keep up with the literature. To do that, you need to have at least a basic level of informatics skills in order to parse and align data, and make some statistical analyses of your own.

As for how to get into it, I find that It’s hard to motivate yourself when you don’t have a specific purpose. It helps to have a biological question in mind, and to learn informatic strategies to help you solve that problem. When I first started learning bioinformatics it was because I wanted to see where this mark was and how it was changing across the cell cycle. To do that I had to learn whether I should be using peak calling, previously created algorithms to call enriched regions, or whether I should simply go and look at the signal and do some straight subtraction. A lot of it is learning by doing it for a purpose. And it never hurts to take a few courses so that you understand the basic steps of dealing with sequencing data.

As a recent PhD graduate, do you have any general advice for incoming graduate students?

A good line of advice that I wish someone had told me when I first started is not to feel discouraged if you have to switch directions. Don’t think of it as a failure. The trade-off for giving up early and pursuing a different project is that it often winds up being more fruitful in the long term.

Thank you for taking the time to discuss your research, Carol! We wish you the best of luck as you move forward in your scientific career!