I have in my RNA-seq quantification data from Arabidopsis obtained by mRNA-seq polyA enrichment library transcripts encoded by chloroplast and mitochondrial genes in significant DEG. How is it possible, if chloroplast and mitochondrial transcripts do not have poly-A tail? Are these data reliable or contaminants which should be ignored?
Do you mean expression from genes that are encoded on the mtDNA or cpDNA or gDNA genes that have proteins that are transported to the mitochondria and chloroplasts?
Most of the proteins found in mitochondria and chloroplasts are coded for by genes in the nuclear genome.
FYI, human mtDNA transcripts do have polyA tails. Not sure if that's true for plants as well, but it's worth a literature search to find out.
I mean genes that are encoded on the mtDNA or cpDNA. I know that in plants some of these transcripts in chloroplasts have heterogenous polyA as signal for degradation. But I do not know how to intepret the data from RNA-seq. Is the quantification reliable as is for nuclear encoded genes?
I checked it and I probably found the response: Moreover, polyadenylation is often
a degradation signal in organelles, meaning that researchers
using poly(A)-selected RNA-Seq for measuring differential
expression in organelle systems may, in some instances,
be measuring the opposite: differential degradation (Smith and Lima, 2016).
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