What is Transcriptomics and Why is it Important? Here’s what Dr. Cartwright has to Say!
By Ameesha Hazarika
Many of us can agree that we have heard of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) and their role in protein synthesis and gene expression. Whereas genomics studies an organism’s genome or the entire DNA sequence, transcriptomics studies all RNA transcripts that are being produced under a certain condition. The entire collection of mRNA sequences in a cell, or the transcriptome, allows scientists and researchers to determine when and where genes are turned on and off in an organism.
For her dissertation, Dr. Cartwright applied her expertise in transcriptomics to analyze the Evolution of Gene Expression Regulation at the Transcriptional and Post-Transcriptional Levels in the Early Drosophila Embryo. More commonly referred to as fruit flies, Drosophila is a genus of flies that is considered a model system for understanding developmental and fundamental genetics. In her time as a postdoctoral teaching scholar with the Biotechnology Program, Dr. Cartwright taught alongside different professors and also collaborated with graduate and undergraduate students to help shape her course on transcriptomics.
“A lot of my grad work was using transcriptomic datasets in order to understand gene regulation. It’s really cool how you can leverage massive amounts of data that you get from sequencing all of the RNA in a sample in order to answer scientific questions.”
Dr. Cartwright
During the BIT SURE program in the summer of 2023, Avni Arora, an undergraduate under Dr. Cartwright’s mentorship, became “instrumental in setting up a lot of the computational pipelines” for her course on transcriptomics she introduced in Fall 2023. Working with a transcriptome means working with a very large dataset that requires bioinformatic pipelines or algorithms to analyze and process the many mRNA sequences. Addressing large datasets can be overwhelming, which is why Dr. Cartwright incorporated a journal club into her course which allowed students to annotate primary literature from scientific journals and raise discussion questions through interactive software such as Perusall. Being able to discuss the various uses of transcriptomics helped students enjoy working with the large datasets and applying it to the course and work in their own research labs.
The wet lab affiliated with her course used Drosophila, specifically Drosophila melanogaster, for students to apply their transcriptomic techniques and add RNA sequencing to their digital portfolio. RNA extraction is achieved when the flies are squished in a buffer and the squished flies (lysate) is then run through a column in a process called column purification. The column has a membrane (silica) which the RNA binds to and then a buffer is passed through the column to remove any unbound contaminants. In the final step of elution, the bound RNA is washed in an aqueous solution and then put in a centrifuge which then allows us to extract and collect the RNA.
Transcriptomics functions as a hypothesis generator; the extensive data gives rise to new questions in the field of genetics. Clinically, transcriptomics has assisted doctors with diagnoses by identifying biomarkers of diseases. Agriculturally, identifying how plants are affected by biotic and abiotic stressors allows for the development of new crops with improved traits. Although there are still some limitations, such as degradation and fragmentation of the RNA within formalin-fixed-paraffin-embedded (FFPE) tissue (a method used to preserve cellular information and tissue morphology), transcriptomics can be applied anywhere to better understand life, how it functions, and how changes in genes contribute to the overall health of the organism.
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