June Update: Change of Plans

Upon returning to campus to begin my project, I found out that new data related to my project had been found while I had been away. This new data identified 398 genes whose transcription was affected (either up or down regulated) by aggregated Huntingtin’s protein (Htt). Also included was the reversal of the negative effects of Htt when a gene known as Slx5 was over-expressed. There is a lot of background information required to understand why these findings are so important.

First, Huntington’s disease is a neurodegenerative disease caused by the aggregation of a mutated protein known as Htt. I spoke a bit about this in my abstract. Any aggregated protein causes stress on the cell in many ways; one way that mutated Htt causes stress is in the nucleus, where it alters the transcriptional regulation of many genes. This abnormal transcriptional activity in the presence of mutant Htt was recorded in the new data set.

Second, cells have developed many ways to handle troublesome aggregated proteins. It is probable that there are certain proteins in the cell that are specifically equipped to handle the harmful effects of mutated Htt. Dr. Oliver Kerscher’s lab has been studying one of these proteins, known as Slx5. They have previously found evidence that over-expressing Slx5 prevents mutated Htt from latching onto DNA and messing with transcription. This new data set further supported this idea by establishing the transcriptional effects of mutant Htt, then showing these effects reversed in a cell with mutant Htt and over-expressed Slx5.

My original project was to develop and use an assay to identify more proteins that alter the effects of mutant Htt, similar to Slx5. However, this new data requires a shift of focus back on to Slx5, to better understand this protein in particular, and verify the new findings. This month has been about interpreting this new data, as well as obtaining my own data to verify the findings. Ultimately, I hope create graphical representations using my own data that show the relationship between Slx5 and the transcriptional activity of mutant Htt.

In order to interpret the new data, I have used several databases of yeast genes to sort the 398 genes by the location their protein products are active. This will aid us in searching for patterns in the kinds of genes mutant Htt affects. This is been my focus this month.

In order to create my own data, this month has been mainly focused on purifying RNA from yeast cells with mutant Htt, as well as yeast cells with both Slx5 and mutant Htt. This part of the project will be the focus in July, and I will walk through my procedures and explain the process in my next blog post.

Overall it has been a productive month, focused on reorienting myself with a new perspective on the problem, and diving in to new data.