I'm trying to come up with an idea for a school project (a hypothetical research study).

I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human cerebellum. There are 2 common alleles of this gene, a "long" and "short" version. The difference is that the long version has 16 repeats of a certain sequence in the promoter, and the short has only 14 repeats. Though there have been some controversial findings, the short genotype has been linked to patients with depression, suicide, less serotonin uptake, and less localization of the serotonin transporter at the cell membrane (synapse). My hypothesis is that RNA polymerase binds preferentially/more strongly to the long allele's promoter over the short allele's promoter in human cerebellum neurons.

This would explain higher levels of transcription of the serotonin transporter gene (though this hasn't actually been shown) and increased serotonin uptake (has been shown), resulting in lowered susceptibility to depression. I was thinking I would do this using ChIP. I would get cerebellum tissue from deceased patients of each genotype (long/long, long/short, short/short) and compare bound RNA-pol in the different genotypes.

My two questions are:

  1. Is this a reasonable hypothesis (does it make sense based on what I have described)?
  2. Hypothetically, is it possible to do ChIP on dead brain tissue?
  • $\begingroup$ I don't know anything about SERT, but your hypothesis sounds plausible to me. However, if you want to determine relative transcription levels, RNA-seq may be more appropriate. I believe ChIP would tell you whether or not RNAP binds the promoter and where, not necessarily how well it binds. Furthermore, I feel that addressing whether or not the transcription level is actually affected may be the step to take before determining why its affected. $\endgroup$ – canadianer Apr 20 '14 at 4:35

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