▲ Seoul National University Department of Mechanical Engineering Professor Yongdae Shin, doctoral student Kim Tae-hyun

-Identification of RNA aggregate density control function
-Published in ‘Nature Communications’, a world-renowned academic journal

Seoul National University College of Engineering (Dean Yoo-Seok Hong) announced that a research team led by Professor Yong-dae Shin of the Department of Mechanical Engineering discovered the existence of low-density liquid droplet aggregates within cells and identified the fact that RNA is important in regulating their density.

The cell interior is spatially compartmentalized by various organelles with unique functions. In addition to membrane-encased organelles such as the nucleus, mitochondria, and endoplasmic reticulum, there are various organelles without membranes such as the nucleolus, nuclear speckle, and stress granules. It has recently been identified that organelles without membranes are liquid droplets formed through phase separation of biomolecules such as DNA, RNA, and proteins, and have attracted great attention from the academic world. The structure is called a phase-separated condensate. Recently, many studies have revealed that biophysical changes or abnormal formation of phase-separated aggregates are closely related to cancer diseases and neurodegenerative diseases.


<Discovery and structural characterization of intracellular low-density aggregates>

The research team acquired biomolecular density information through 3D refractive index measurement to understand in depth the biophysical characteristics of phase-separated aggregates in living cells. The biomolecule density distribution was measured for representative aggregates such as the nucleolus, heterochromatin, nuclear speckle, and stress granule. Contrary to the general prediction that aggregates are formed by concentrating specific biomolecules, the density is higher than that of the surrounding area. In the case of nuclear speckles and stress granules, it was found that they are low-density aggregates with similar densities to the surrounding area.

The research team paid attention to the behavior of these low-density aggregates and further studied their structural properties and density control mechanisms. Since biomolecule density is the total mass of biomolecules contained in a unit volume in a structure, low density of a specific aggregate suggests that there are relatively many empty spaces inside it. To confirm this, a fluorescent protein probe was co-expressed inside the cell, and how much of the protein probe could enter the aggregate was measured. As a result, it was observed that it was difficult for the protein probe to approach the inside of the high-density aggregate, but easily entered the low-density aggregate. Based this, it was confirmed that the low-density aggregates have a strong internal structure.

The research team further traced the principle by which low-density aggregates could be created. Since physical interactions and connectivity between biomolecules are required to maintain aggregates, it was hypothesized that RNAs with longer structures than proteins would play an important role in low-density aggregates. As a result of an experiment to remove intracellular RNA, it was observed that the density of aggregates increased as RNA was removed, and at the same time, the internal space became more compact. Through this, the researchers discovered that RNA plays a key role in regulating the density of aggregates.

Through this study, we were able to understand the biophysical characteristics of cell organelles without intracellular membranes in more depth. Based this achievement, the research team will continue to study the biophysical characteristics of aggregates and link them with diseases, discover new aggregate-based therapeutics, and apply synthetic biological applications in the future.

In recognition for these achievements, the results of this study were published April 27^th in the world-renowned journal Nature Communications.

[Thesis title] RNA-mediated demixing transition of low-density condensates

[Inquiry]
Seoul National University College of Engineering, Department of Mechanical Engineering, Ph.D. Candidate Taehyeon Kim / 02-880-1906 / taehyunkim20@snu.ac.kr