I am Eslim Esra Alpay, a research technologist in Özbudak Lab since October 2021. This article is very special to me as it is my first first-author paper. It is also special in another way – it allowed me to employ single molecule fluorescent in situ hybridization (smFISH) technology, which was the first technique I learned in my post-bachelor career,  as its basis. Our research investigates the distinct functions of DeltaC and DeltaD ligands in segmentation clock in the zebrafish embryo during development. Somites will form periodically in the control of segmentation clock, and these structures are leading vertebral disc formation.

The challenge of this project was the combination of smFISH experiment, confocal microscopy imaging, and single-cell analysis. Although these experiments were time-consuming, they provided precise quantification of transcript numbers.

To understand the distinct functions of DeltaC and DeltaD in regulating the transcription of clock genes her1 and her7,  a non-oscillating background was used. Earlier research had indicated that only dimers containing DeltaC were functional, as DeltaC was reported to oscillate. But our findings showed something surprising: DeltaD homodimers are also involved in gene expression. Furthermore, we uncovered a novel positive feedback mechanism in Notch signaling that is accountable for the regulation of deltaC and deltaD transcription as well.

We also collaborated with Dr. Ahmet Ay’s group and used computational modeling to interpret the effects of the DeltaC and DeltaD ligands on synchronization of the segmentation clock. Our model supported our experimental findings and revealed that the two ligands affect gene expression differently. Previous studies have shown that the boundary phenotype in deltaC mutants develops earlier than the broken boundary phenotype in deltaD mutants, and we confirmed these findings with our computational modeling.

While this research provides valuable insights, it also raises new questions. There is still much to discover, and I am excited about the potential future breakthroughs that may arise from further exploration inspired by this paper.

You can also check out our lab’s tweet about this study: Özbudak Lab Twitter Post.