Measuring live gene expression of two spatially coupled sister chromatids
Hernan Garcia, Professor
Molecular and Cell Biology
Applications for Fall 2025 are closed for this project.
Gene expression is noisy. How much of this noise is due to variations in the environment of a gene locus, and how much is due to intrinsic limitations of the transcriptional machinery? This project aims to explore these questions by measuring the transcriptional dynamics of two identical, spatially coupled reporter constructs – sister chromatids.
In the early fruit fly embryo, the DNA in each nucleus is duplicated prior to the onset of transcription. As a result, even measurements of transcription with single-nucleus resolution must report on a sum of activity between two sister chromatids that are too close together to resolve. Is transcription between the chromatids coupled positively, negatively, or not at all? Evidence for all three paradigms has been found by conflicting studies over the past 50 years. In this project, we will harness recent advancements in genetics, microscopy and analysis to build a platform to investigate the dynamics of single-chromatid gene expression within live, developing fruit fly embryos.
Role: A student on this project will learn:
- Fly genetics and maintenance: organizing genetic crosses and feeding stocks of fruit flies
- Sample collection and preparation
- Microscopy: setting up the experiment and doing live imaging of developing embryos
- Image analysis: segmenting and tracking images using our lab’s existing Python pipeline
-Computational inference: extracting the precise timing of transcription initiation events from datasets
- Model building and data analysis: comparing single chromatids to pairs of chromatids, and predicting models for coupled expression
- Writing: summarizing results and conclusions
Qualifications: Qualifications: Python (helpful but not essential)
Major: Molecular Cellular Biology, Bioengineering, Chemical Biology, Integrative Biology, Genetics and Plant Biology, Physics
Day-to-day supervisor for this project: Andrea Herman, Ph.D. candidate
Hours: 9-11 hrs
Biological & Health Sciences