Question

If A a transcription factor or B a response element in a gene were mutated and not functional, how could transcriptomics by RNA-seq or cDNA microarrays be used to find which gene(s) was/were affected? Which method (RNA-seq or microarrays) is better and why? Explain your answers for both A and B in detail and be sure to address how the results of A versus B would likely differ from each other.

Answer 1

First, we should take into account that RNA-seq allows us to identify the mRNA sequence and its expression level in the cell, while cDNA microarrays allows us to know the relative expression of a gene. Moreover, for this explanation, I will assume that the transcription factor acts as an activator, that is, it promotes mRNA synthesis of a specific gene by binding to DNA and forming stable interactions with RNA polymerase.

Since RNA-seq is more accurate, it allows a deeper analysis, easier data analysis and allows us to find out which gene was mutated. it seems better than cDNA microarrays.

It is hard to say if there will be differences with cDNA microarrays in Case A and B because there can be other factors altering gene expression, such as other transcription factors or proteins involved in DNA polymerase recruitment, or the noise caused by incorrect probe hybridization with undesired gene products. However, this technique would allow us to know that a mutation occurred because we would detect low activity levels in both cases.

If we apply RNA-seq in both A and B, we would expect to see low expression levels, since this technique is more specific and accurate in quantitative terms. By applying this technique, however, I would expect to detect differences in expression levels between case A and B. It might be that expression level in case A is greater than expression level in case B because there could be other family of transcription factors able to bind to the not mutated response element.