Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Arjun Raj


Biological variability is often treated as a drawback of biological systems, but we have used it to learn about various biological phenomena, such as mesenchymal stem cell variability and the timing of splicing. We quantified the variability of mesenchymal stem cell clones with respect to their ability to generate cartilage-like extracellular matrix tissues and used this variability to identify markers that could be used to sort cells that produce high quality cartilage tissue. This revealed that canonical markers commonly used in cartilage tissue engineering are poor markers of high performing mesenchymal stem cells, suggesting that sorting cells based on these markers will not enrich populations for cartilage tissue production. We also used RNA FISH to characterize single-cell level expression of these markers and found that the expression showed high variability and very little cell-to-cell memory. RNA FISH also revealed that during de-differentiation of chondrocytes in monolayer culture, expression of canonical markers does not decrease on the absolute level, but only relative to cell size, also suggesting the gene expression level of these markers is not the sole determining factor for the production of high-quality cartilage tissue.

I then decided to use RNA FISH to quantify the gene-to-gene and intron-to-intron heterogeneity in splicing that occurs at and near the site of transcription, revealing a spectrum of co- and post-transcriptional splicing of endogenous genes. Observing multiple introns of the same gene simultaneously showed that introns are largely spliced independently of one another and not in a 5’ to 3’ order. Using a combination of RNA FISH and expansion microscopy, I show that transcripts dwell at the transcription site after transcription is complete, suggesting that fractionation methods may underestimate “post- transcriptionality”. Taken together, our observations suggest a model of dwell time at the site of transcription, variable intron retention, and a sequence-specific regulation of the timing and localization of splicing for individual introns.

Files over 3MB may be slow to open. For best results, right-click and select "save as..."