This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is a transcriptome?
Your genome is your DNA, which codes for specific RNAs which in turn code for proteins. That is the central dogma of biology and genetics, and is illustrated on the right. When your DNA is 'read' by an RNA polymerase, the product is an RNA. [1] This RNA is logically called the transcript. The compilation of all of these RNA reads is called the transcriptome. [1] Transcriptomics is the study of the transcriptome. [1]
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What can we do with transcriptomics?
Information about the transcript can be interpreted in several ways. One of which is called RNA sequencing. RNA-seq is a highly sensitive technique for detecting changes in gene regulation. [2] Gene regulation is referring to expression of the particular gene; an upregulated gene is expressed more while a downregulated gene is expressed less.
RNA-seq is useful when comparing the transcriptome changes in a tissue under two different conditions. For example, it would be useful to compare the expression of TGFB1 in nasal tissue before and during an allergic response. The picture on the left is one type of readout from an RNA-seq, called a heat map. Each horizontal row on the map represents a different gene, while each vertical column represents a replicate. The colors on the map identify which genes are upregulated or downregulated in each replicate. [2] |
How can we use RNA sequencing?
Comparing gene expression in tissue from a healthy person to a person who suffers from allergic rhinitis is important in our study of the disease for many reasons. The process we use to compare is shown on the right. [5] As you can see, there are different ways to compare cellular level expression and tissue level expression of the gene causing the disease pathology. We would expect gene expression to change when an animal is having an allergic reaction, as compared to when it is not. Transcriptomics can tell us more about those changes in gene expression.
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Analysis
The transcriptome is a vital tool in understanding gene regulation and disease phenotypes. We can employ the study of transcriptomics to run RNA sequencing experiments which allow us to compare cells or tissue of a healthy person to that of an allergic person. We can use a heat map to show us the specific upregulation or downregulation of genes involved in allergic rhinits. Transcriptomics for allergic rhinits is useful in understanding what cells do in response to stimulation by an allergen. If we can understand what genes like TGFB1 do in these circumstances, it gives us a basis of information to form a hypothesis about why they behave this way and how to fix it.
References
[1] National Human Genome Research Institute. Transcriptome. Aug 27 2015.
[2] Illumina. Next-Generation Sequencing (NGS). 2017.
Images
[1] http://diagram.aveniqueserumbuy.com/central-dogma-diagram-of-molecular-biology/
[2] http://genetics564.weebly.com/gene-expression-analysis.html
[2] Illumina. Next-Generation Sequencing (NGS). 2017.
Images
[1] http://diagram.aveniqueserumbuy.com/central-dogma-diagram-of-molecular-biology/
[2] http://genetics564.weebly.com/gene-expression-analysis.html