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 the RNA in a cell. It tells you which genes are being transcribed in each cell. This is often studied using a microarray, qRT-PCR, and RNA-seq. In all of these techniques, RNA first needs to be reverse transcribed into cDNA. In a microarray, small fragments of the DNA of interest are placed on a surface, then the fluorescently tagged cDNA is washed over it and will hybridize to any complementary sequences. The strength of the fluorescent shows if and how much the cDNA is binding. qRT-PCR first converts the RNA of interest to cDNA and then amplifies and measures the amounts present. These two techniques are useful for finding out if known sequences are expressed. To discover novel sequences, RNA-seq must be used. In RNA-seq, the RNA is converted into cDNA which is then sequenced. [1]
Transcriptomics and MSH6
Utilizing GEO Profiles and DataSets, which show gene expression profiles, level of MSH6 expression under different conditions can be explored. Additionally, genes that have similar expression with MSH6 under certain conditions can reveal processes that MSH6 could potentially be involved in.
Figure 1: Profile showing level of MSH6 between colorectal tumors with microsatellite instability and normal colonic tissue
Figure 2: Heat map showing differential expression of genes in early and late onset colorectal cancer. Pink corresponds with higher expression and green with low expression.
Conclusions
Based on GEO profiles, it can be seen that MSH6 has higher expression in colorectal cancer with microsatellite-instability and in early onset colorectal cancer. These results support what is already known about the contribution of MSH6 to the development of colorectal cancer. Additional explorations of MSH6 expression in relation to other mutations yielded conflicting data.