This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is transcriptomics?
Transcriptomics is the study of all of RNA molecules (transciptome) in the molecule. [1] This can be focused on a specific type of RNA, for example mRNA, or the analysis can be done with the entire transciptome. [1] Transcriptomics allows the scientist to see different expression levels of a certain RNA in different conditions. These different conditions could be different organelles, cell types, or even different testing conditions. Differing gene expression, measured by mRNA count, is valuable information when you're trying to build a model of how a gene interacts with its environment and how that environment interacts with it. The main method of obtaining RNA expression levels is through RNA-sequencing.
RNA Sequencing
RNA sequencing (RNA-seq) is quickly becoming a valuable tool in a geneticists toolbox. It involves first converting the mRNA (or any RNA) to its complementary DNA (cDNA) by using an extensive cDNA library. This cDNA then undergoes next-generation sequencing to create a library of cDNA from the isolate RNA. This library is then aligned to the genome and the cDNA are counted to determine relative expression. [2] |
Transcriptomics and TMC6
Mutations in TMC6 are known to be some of the most important factors regarding the pathology of EV. EV is a dermal (skin) disease that is characterized by the lack of innate cellular-mediate immunity to beta-HPV. This being said, it is likely that TMC6 is expressed highly in both the skin and potentially the immune system. Using The Human Protein Atlas the expression levels of TMC6 in different cell types are able to be visualized. It shows that TMC6 RNA is expressed highly in immune-related cell types, but is expressed at a much lower amount in the skin relative to the immune-related cell types. [3] This suggests that TMC6 has multiple different roles in the immune system and throughout the body and that it is not localized to only beta-HPV immunity in the skin.
Conclusion
Transcriptomics is critical to the understanding of a gene's functions because it allows its expression levels to be critically analyzed. How much a gene is expressed, where its expressed, and what other genes are expressed similarly are all important questions that can be answered through the use of transcriptomics. This makes it extremely valuable while performing experiments. For example, TMC6 is hypothesized to stabilize CIB1 and regulate CIB1 levels post-transcriptionally. With RNA-seq, expression levels of not only TMC6 can be obtained but also of CIB1. This can be used in combination with CRISPR or another genetic engineering technique to understand the relationship between CIB1 expression and TMC6 when it is knocked-out or mutated. This information could be critical to the understanding of this interaction.
Sources:
1. http://www.phgfoundation.org/blog/what-is-transcriptomics
2. https://bitesizebio.com/13542/what-everyone-should-know-about-rna-seq/
3. https://www.proteinatlas.org/ENSG00000141524-TMC6/tissue
Figures:
https://www.google.com/url?sa=i&source=images&cd=&cad=rja&uact=8&ved=2ahUKEwjtk6eDuYLhAhUi44MKHdTFApsQjhx6BAgBEAM&url=http%3A%2F%2Fwww.pathologystor ybook.com%2Ftag%2Fcentral-dogma-of-biology%2F&psig=AOvVaw391mIYMqqgY3_KsFBtNe8K&ust=1552680820269268
1. http://www.phgfoundation.org/blog/what-is-transcriptomics
2. https://bitesizebio.com/13542/what-everyone-should-know-about-rna-seq/
3. https://www.proteinatlas.org/ENSG00000141524-TMC6/tissue
Figures:
https://www.google.com/url?sa=i&source=images&cd=&cad=rja&uact=8&ved=2ahUKEwjtk6eDuYLhAhUi44MKHdTFApsQjhx6BAgBEAM&url=http%3A%2F%2Fwww.pathologystor ybook.com%2Ftag%2Fcentral-dogma-of-biology%2F&psig=AOvVaw391mIYMqqgY3_KsFBtNe8K&ust=1552680820269268