Hi, my question is about normalization data from ChIP-qPCR using the gene copy number.
I did ChIP-qPCR for several histone marks on tRNA-Met and tRNA-Arg genes that are in the same chromosome (close to each other), and different areas close to these tRNAs. In order to describe the distribution of this histones mark across these regions.
There are 5 copies of tRNA-Met in all the genome, and only 2 copies of tRNA-Arg.
My question is: I need to normalize the enrichment according the copy number of these tRNA genes?
The primers used to amplify in qPCR the tRNA-Met and tRNA-Arg genes can amplify copies in other chromosomes (Not are specific to one locus-copy).
Thanks for your support.
Hi Juan Carlos,
I face the same question for 5S rDNA.
The conclusion was that as long as you normalize your IP with H3/H4 or with input, it will give you the average enrichment for 1 copy (as you will divide by the number of DNA molecule for all the copies). So you don't need to normalize again by the copy number.
Cheers
Lauriane
Hi Simon thanks for your support.
I normalized using IgG and H3 (for nucleosome density).
Best whises
JC
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