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I'm interested in knowing how many Pol II molecules are simultaneously transcribing any given gene. There are RNA pol II ChIP-seq (phospho-S5) data for different cells but these come from pooled cell samples. So the different peaks on any given gene would be the average of the cell population. Single cell ChIP-seq data would help but I can't find any.

The other way to check this is to calculate transcription rates of different genes, normalize with copy number and divide by the elongation rate of the polymerase on that gene. However, elongation rate is not unique for all genes.

Is there any resource – paper or raw data, which would help me find the answer to the question?

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Regulation of RNA polymerase II activation by histone acetylation in single living cells by Stasevich et al. provides detail on how they were able to determine the number of elongating RNA polymerase II for a given gene array. The issue I had with the paper is that they used a ~1.8Mbp tandem repeat as their target, so they really upped the probability of seeing activity. You may be able to do similar for your gene of interest, but there may not be enough signal to tease out your data.

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