Defining how pluripotency is controlled in real time

A/Prof Jenny Zenker and team awarded ARC Discovery Project to reveal how RNA dynamics steer the earliest cell fates

Why the earliest decisions matter

When an embryo is only a handful of cells, each cell must quickly decide its future: become part of the embryo proper (pluripotent and able to make any cell type), or contribute to supporting tissues like the placenta. How those decisions are made and how to see them as they happen is the focus of a new Australian Research Council (ARC) Discovery Project led by Associate Professor Jennifer Zenker at the Australian Regenerative Medicine Institute, Monash University.

Backed by $860,456 over four years, the project will develop gentler, real-time imaging tools to watch RNAs and proteins move inside living embryos and stem-cell models and test whether simply changing the mix of RNAs can tip cells toward or away from pluripotency.

A first in mammals

The Zenker lab recently showed that, in mouse embryos, the cell’s RNAs don’t sit evenly inside the cytoplasm during a crucial transition (from 16 to 32 cells). Instead, it pools to one side.

When that cell divides, the two daughter cells inherit very different RNA “loads” and tend to adopt different fates: the RNA-rich daughter remains pluripotent; the RNA-poor daughter heads toward extra-embryonic roles.

It’s the first demonstration of such RNA asymmetry linked to fate in a mammalian embryo, expanding a principle long known in non-mammalian systems like fruit fly development. Demonstrating a clear RNA asymmetry linked to fate bias in a mammalian embryo is the step forward that sets up this project.

What is RNA, and why this is different

RNA is the working language of the cell. Messenger RNA carries instructions to make proteins, transfer RNA helps assemble them, and ribosomal RNA forms the core of the protein-making machinery. Classically, RNA is treated as a messenger that reflects what the DNA has ordered. This project treats RNA as something more: a spatial and compositional signal. Where RNA sits inside a living cell, and the balance between its types, may help set the fate of that cell before genes are turned on or off in the usual way.

How we will see RNA move

The lab will develop gentle, real-time imaging tools to watch where different RNA classes sit inside single cells as a mammalian embryo develops. Working with chemists at the University of Sydney, including Dr Liam Adair in Professor Elizabeth New’s laboratory, the team will create fluorescent probes for messenger RNA, transfer RNA and ribosomal RNA, designed for living cells and paired with careful optics to avoid harming normal development.

Dr Hongbin Jin, in the Zenker lab at ARMI, leads the microinjection and live-imaging techniques that makes this possible. He uses a custom microinjector rig to deliver tiny amounts of RNA and probe chemistries with precision, while keeping embryos healthy for hours to days of observation. Hongbin also runs the image-analysis pipeline, so the team can quantify where RNAs go and when translation turns on.

The experiments span two settings. In mouse embryos, the team will capture the in vivo dynamics during the sixteen cell transition. In human-relevant systems, they will repeat key tests in models that let researchers study early decisions without using human embryos. These models include induced pluripotent stem cells, which are adult cells reprogrammed back into a flexible state, and iBlastoids, which are tiny structures grown from human cells that mimic some features of a very early embryo in a dish. Using these complementary systems lets the team test whether the same rules of RNA localisation and translation hold across species and contexts.

Watching translation in its moment

Location is only half the story. The project will also measure when and where proteins are made. By tracking brief bursts of translation in vivo, the team will relate timing and duration of protein production to the emergence of cell fates. This brings the field from single snapshots to dynamic, quantitative readouts.

Testing whether RNA composition helps set fate

A central idea of the project is that the overall balance of RNA types inside a cell may help maintain pluripotency. Pluripotent cells appear unusually rich in ribosomal RNA, which fits this view. Using the lab’s custom microinjection and live-imaging platform, the team will explore controlled ways to adjust RNA composition and then watch, in real time, how localisation and translation dynamics relate to emerging cell identities. The goal is to learn whether RNA composition can be part of the mechanism that guides fate, and to do so with methods that are gentle and reversible.

“Most tools change DNA to study pluripotency. We’re asking if tuning the RNA mix, without touching the genome can gently steer cell fate. If true, that opens a new, less invasive playbook,” says A/Prof Zenker.

Benefits without clinical claims

A systems-level view of RNA and translation in living embryos can sharpen quality control in pluripotent cell culture, improve toxicology and drug screening workflows, and provide faster ways to detect abnormal embryonic cells. Insights into developmental robustness can inform breeding programs for endangered wildlife and support sustainable livestock management. The work also strengthens the knowledge base for research relevant to Australia’s historic fertility decline and healthy ageing, while remaining firmly focused on fundamental science.

Looking ahead

This is the first clear demonstration of RNA asymmetry linked to fate bias in a mammalian embryo, and it is a big step. The next horizon is to test whether the same rules apply in other mammalian systems. With live probes and precise microinjection in hand, the team will extend studies from mouse to human-relevant models and, where appropriate, to higher mammals used in conservation and agriculture. Success means confirming conserved principles of RNA-guided fate, refining tools so other labs can adopt them with ease, and building partnerships that translate fundamental insights into real gains for wildlife breeding and sustainable livestock management. The work will also strengthen the knowledge base that informs research on Australia’s fertility trends and healthy ageing, while establishing Monash as a leader in live, minimally disruptive studies of pluripotency.

About ARMI
The Australian Regenerative Medicine Institute (ARMI), based at Monash University in Melbourne, is a world leader in regenerative biology and stem cell research. ARMI works at the frontier of science, translating discovery into hope for people living with conditions like cancer, arthritis, and neurological injury.

Media Contact:
Emma Burrows, Communication Consultant ARMI.
M: 0417431376
E: emma.burrows@monash.edu