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 gene expression (transcription) or the study of the transcriptome. A trsncriptome is all total RNA in a cell or population of cells [1]. By analyzing the RNAs being transcribed in a cell, researchers are able to identify which genes are active in a given cell or population. Researchers can also use the transcriptome to try and identify a gene's function [2].
What is RNA sequencing?
RNA sequencing (RNA-seq) is a technique to reveal the presence and quantity of RNA in a cell or cell population [3]. This technology allows for more precise quantification of RNA levels in cells. The way RNA-seq works is to change unstable RNA into complementary DNA (cDNA) fragments. These fragments have adaptors on one or both ends. The cDNA fragments create short reads (30-500 bp) and aligned to produce a genome-wide transcription map [1]. The transcription map gives information about the structure and gene levels in the genome.
How transcriptomics can be used to study LXRA.
Transcriptomics is important to understand how a single cells or tissue is expressing genes. It can be even more powerful when comparing different tissues or comparing wild type and mutant. In particular, I am interested in looking at how mutation in the LXRA gene contributes to MS in a mouse model. Using transcriptomics, I can test the expression levels of LXRA in wild type and diseased mice. LXRA has been shown to be active in all tissues. It is highly expressed in the liver, adipose tissue, and macrophages. Using this information, we may be able to develop better drug therapies for patients with multiple sclerosis.
References
[1] Wang et al. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63
[2] Transcriptome Fact Sheet. (n.d.). Retrieved March 15, 2018, from https://www.genome.gov/13014330/transcriptome-fact-sheet/
[3] Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics, 10(1), 57–63. http://doi.org/10.1038/nrg2484
[2] Transcriptome Fact Sheet. (n.d.). Retrieved March 15, 2018, from https://www.genome.gov/13014330/transcriptome-fact-sheet/
[3] Wang, Z., Gerstein, M., & Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics, 10(1), 57–63. http://doi.org/10.1038/nrg2484