Ibrahim Cissé Tracks Molecular Condensates in Super Resolution

Understanding how the world around him works has always fascinated Ibrahim Cissé, a biological physicist at the Max Planck Institute for Immunobiology and Epigenetics. Cissé’s curiosity first led him to tackle hard-to-solve mathematical and science problems, such as determining how to optimally pack objects to fill a volume. For this, he devised an ingenious solution by filling a jar of M&M candies with paint, letting it dry, and then removing the candies to count the number of spots missing paint; these indicated contact regions between the M&Ms. Cissé showed that the bite-sized ellipsoidal chocolate candies packed more densely than perfect spherical objects.¹

When The Scientist first featured Cissé’s work in 2020, he had developed microscopy tools that allowed scientists to overcome the physical optical limits that make small molecules indistinguishable from one another. These methods, such as Photoactivated Localization Microscopy (PALM), allowed Cissé to capture transient contacts that molecules make as they assemble and disassemble to regulate gene expression.

In honor of The Scientist’s 40^th anniversary, we spoke with Cissé again to see what paths his curiosity-driven research has taken. Using super-resolution microscopy techniques, his team continues to investigate the ephemeral dance of molecules that control transcription. They are also applying these and other newly developed microscopy methods to understand how transient molecular interactions emerge inside cells and influence biological processes.

A Kiss From a Transcriptional Condensate

In his early work, Cissé described how RNA polymerase II, a key enzyme for transcription, forms transient clusters or condensates with other molecules around genes being transcribed; he and his team also discovered that the amount of time the clusters lingered around these genes correlated with the number of mRNA molecules produced inside cells.^2,3 While these findings suggested that the RNA polymerase clusters could influence gene expression, whether they actually played a role in the process or were just aggregating inside the cells was an open question, Cissé explained.

To determine the role of RNA polymerase clusters inside cells, Cissé’s team developed a live-cell super-resolution microscopy approach that allowed the researchers to simultaneously mark the nascent mRNAs and the super-enhancer region of the SRY-box transcription factor 2 (Sox2) gene, which is essential for embryonic development. The team found that when the Sox2 super enhancer, which is located far away from the gene, loops close to the Sox2 gene, there is a basal burst in mRNA production that increases when the RNA polymerase II cluster sneaks in and “kisses” the gene.⁴ “[This] was really as direct as we can hope to capture how the condensates would correlate with the real-time gene expression regulation,” Cissé noted.

While Cissé’s work has primarily focused on how transcriptional clusters composed of RNA polymerase and other molecules emerge and regulate gene expression, his team has also sought out other naturally occurring protein clusters outside the nucleus. They are applying their super-resolution technologies to understand their roles too.

Condensates in Neurodegenerative Diseases

Back at The Massachusetts Institute of Technology (MIT), where Cissé worked as a principal investigator from 2014 to 2020 before joining the Max Planck Institute in 2021, he teamed up with Ariel University molecular biologist Michael Sherman to explore the emergence of protein aggregates in neurodegenerative diseases. These aggregates are hallmarks of Parkinson’s disease and Alzheimer’s disease, and the two researchers wondered whether they would behave similarly to the condensates Cissé was studying.

Using super-resolution and light sheet microscopy techniques, Cissé’s team showed that mammalian cells, even before protein aggregation was induced, already had the beginnings of protein clusters. “By normal microscopy, it looks like there is nothing happening, but when you do high-resolution microscopy, you start to see a lot of precursors of clusters,” he said.

The researchers found that the distribution of clusters of different sizes could be described by the same physical rules that explain how condensates form. This involves the formation of precursor clusters that assemble and disassemble dynamically before an energy threshold is reached to form large, stable condensates. Cissé explained that, in such a system, a clearance mechanism must monitor the formation of these clusters and get rid of those that reach a critical size, which could throw the system off balance. In their experiments, the researchers identified such a clearance mechanism responsible for disassembling large protein clusters, thus reinforcing the idea that early protein aggregates behave like condensates.⁵

“It was really fantastic, as a physicist, [to] look inside a complex cell and see exactly what you study in your physics textbook,” Cissé said. “It was extremely satisfying to be able to see that in a real experimental system.”

Cluster Formation at the Lab Bench Too

Cissé sees a lot of similarities between his approach to doing research and the dynamic molecular interactions he has spent over a decade studying. While at MIT, for instance, Cissé explained that his team collaborated with scientists interested in exploring genomic structure, which focused his research on RNA polymerase clusters and how they dynamically regulate gene expression. Now at the Max Planck Institute, where Cissé’s team is surrounded by researchers studying epigenetic mechanisms, he is expanding his work to investigate how epigenetics may be involved in controlling RNA polymerase clusters and their role in regulating gene expression.⁶

“You have many different molecules that come in together, and even through their transient interactions, they could emerge into these clusters and condensates that have a function that was not predictable before,” Cissé said. “I think of many of my colleagues that I interact with and my students, postdocs, and other trainees as [a] very similar kind of emergent phenomenon that leads our research to rather unexpected directions.”

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