Friday, June 5, 2015

Does transcription impact recombination?

The short answer seems to be a no.

So I got Josh's recombination data where he gave Haemophilus influenzae 86-028NP donor DNA to KW20 and sequenced 10,000 pooled colonies that had undergone recombination.

I wanted to see if transcription affected recombination (ex. areas of high recombination tend to recombine less) so I made some plots that combined both sets of data:

Here I graphed the % donor alleles as the points. These points correspond to how much recombination is happening. I added some rectangles (genes) at the bottom to orient the graph. The black line corresponds to transcription. The line is the log of the coverage from KW20 at timepoint M0; This is straight from raw read counts. Note there is no axis for the values, but it is plotted on the same scale between graphs. I just wanted to see relative levels of transcription.

I made plots like these for the whole genome:

I went though all of these plots and there does not seem to be any relationship between transcription and recombination at all. If there is an effect of transcription, it is very small and probably not worth looking into deeper at this point.

If interested, I uploaded all 182 plots and the R script I made for this in the Google Drive:
RNAseq docs/Scott/Recombination


Rosie Redfield said...

The variation in the recombination frequencies would be more evident (or perhaps exaggerated) when viewed on a log scale. I don't expect this will reveal anything you missed with the linear axis, but it would be worth checking just to see what it looks like.

Rosie Redfield said...

Since this recombination happened in cell that had been incubated in MIV for 100 minutes, it would be better to use the KW20 M3 data.

Scott M. said...

Good suggestions. If for some reason I need to go back to this data, I'll be sure to add those changes.

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