Question

)You have labelled RNA probes ("riboprobes") directed against the sixth exon of a 7 exon long mRNA corresponding to the Nealosin gene. On a northern blot, you get the appropriate-sized band of 1235 bases from control liver tissue reliably Another scientist in your lab has recently obtained liver tissue from a cancer patient. Since he has some RNA from this sample left over, you decide to throw it on a gel with your sample and your Neolosin-specific riboprobe. In the lane corresponding to the cancer sample, you get no band at all, but you do get the usual 1235 band from your control sample. Additional testing on the cancer sample indicates that the general quality of the RNA is excellent. However, using an antibody to Nealosin, you are able to detect its protein in both samples. What are some possible reasons for this, and how could you test them? Explain in detail one alteration that is at the transcriptional level, and one at the post-transcriptional level.

Answer 1

It is given that a transcript and protein are found in the control sample. However, the transcript is absent but the protein is present in the cancer sample.
The non-detection of the transcript from the cancer sample could be due to alternative splicing in which the 6th exon is skipped. Remember that the probe is specific to the 6th exon. To confirm this, use a probe which is specific against other regions of the transcript. Since the protein is present, the transcript must be present.
The protein is detected in both the sample. This is possible only when the given antibody detects a region which is present in both the WT and alternatively spliced protein. To confirm this, use an antibody which is specific to the C-terminus of the protein and analyze the results.

In some cases, a low level of transcription could be a reason for the non-detection of the transcript in the cancer cells. This could be due to an inactivating mutation in the activator or an activating mutation in a repressor.