First person – Jiah Kim

Jiah Kim

How would you explain the main findings of your paper in lay terms?

The environment in a cell nucleus is very crowded with numerous macromolecules such as RNA, DNA and proteins. Interestingly, biochemical processes occur efficiently in highly organized orders and specific locations even in such a crowded cellular environment. Membrane-bound organelles and membrane-less bodies are involved in functional organization. The former separate their contents from the surrounding environment by using a membrane, but membrane-less bodies are liquid-like bodies, which separate their contents through de-mixing, just like between oil and water. These bodies continuously turn over their constituent molecules, such as RNAs, and proteins which function in transcription, RNA processing and/or protein modification.

Nuclear speckles are one of the membrane-less bodies found in a mammalian cell nucleus. One can find 20–40 irregular-shaped bodies varying in size from ∼0.5 µm to several micrometers in a nucleus. They are immobile and do not significantly change aspects of their morphology, such as shape, size and numbers, during the normal growth phase of a cell cycle. However, when transcription is inhibited, speckles get rounder and larger. We found that they become very mobile and travel long distances, even over several micrometers, in response to transcription inhibition. Movements of nuclear speckles were directional to one another and terminated with fusion, which resulted in a decrease in number and increase in size of nuclear speckles throughout the cell nucleus. These directional movements repeatedly occurred, interestingly, in DNA-poor and speckle material-concentrated nuclear regions. We anticipate these non-random speckle dynamics may provide a rapid and effective transport of RNA processing and/or transcription factors to specific nuclear sites, as well as recycling of speckle components to nuclear speckles and regulation of speckle number and size.

Were there any specific challenges associated with this project? If so, how did you overcome them?

The first challenge was to quantify the change in speckle morphology. To get meaningful quantitative data, we needed to take many pictures of cell nuclei, and to analyze individual speckle morphology. Thanks to an automated microscope system, collecting hundreds of cell nucleus images was do-able, but I could not analyze speckles one by one. To analyze thousands of speckles, I had to learn coding and image processing for the first time. It was a new experience for me but it became a fun part of this project. However, the main challenge was to segment speckles in a variety of sizes and brightness. A single condition such as a size or brightness threshold did not work. I could finally do it through two to three iterations of segmentation, which select from large and bright ones to small and dark ones.

The second challenge was correlative microscopy using three different microscopes. I wanted to know whether there was a correlation between a highly resolved structure of chromatin, speckle material (SON)-concentrated region and locations where directional speckle movement occurred repeatedly. One type of microscope could not give us the answer. Therefore, I used a wide-field microscope (providing high speed of imaging with low photo-toxicity for live-cell imaging), a structured illumination microscope (SIM) (providing good z-resolution for high-resolution chromatin imaging), and a stimulated emission depletion microscope (STED) (providing good x-y resolution for resolving diffraction limited speckle granules). Indeed, speckle movements repeatedly occurred in chromatin-poor and speckle material-abundant regions.

When doing the research, did you have a particular result or ‘eureka’ moment that has stuck with you?

In this study, the most striking aspects of the long-range directional speckle movement were the repeated cycles of speckle nucleation, translocation of the newly nucleated speckles along a trajectory and then fusion with a target speckle. While we observed these events during periods of increased nuclear speckle reorganization induced by transcriptional inhibition or stress responses, similar dynamics were observed under normal growth conditions during the entry into mitosis. During the G2 to early prophase transition, chromatin condenses and the chromatin-depleted region increases immediately prior to mitosis. The entry into mitosis is also accompanied by significant transcriptional repression. As speckles re-organize under transcription inhibition or stress conditions, speckles also dramatically re-organize through directional movements during mitosis. Therefore, we suggest a mechanism for long-range, directional nuclear speckle movements, contributing to overall regulation of nuclear speckle number and size as well as overall nuclear organization.

What motivated you to pursue a career in science, and what have been the most interesting moments on the path that led you to where you are now?

I like to learn and to experience new things. I think science is perfect for this purpose. To solve scientific problems, we have to keep learning and trying different things.

Of course, not all experiments work and results can be disappointing too. Nevertheless, the most exciting moment is when I overcome challenges and get new results, and I can make a hypothesis or plan based on what I have learned. This achievement outweighs all of the disappointing moments that I might go through. I like working in science for this breakthrough moment, no matter how much effort and time it takes.

Tell us something interesting about yourself that wouldn't be on your CV

I like skiing and snowboarding. I sometimes think that the thrills from trying new trails or learning new skills are like those from trying new experiments or testing new scientific models.