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[Arabidopsis] How many genes are transcribed?

Elliot Meyerowitz via arab-gen%40net.bio.net (by elliot.meyerowitz from gmail.com)
Thu Apr 11 12:46:12 EST 2013

I think the answer will depend upon how many different cell types are in your sample - for whole plants and tissues these sorts of measurements have been made often, in several different ways, in the past 35 years (e.g. for tobacco leaves Goldberg et al. Cell 14:23 1978), but the number you really want might be for single cell types, or small numbers of mixed cell types, at single developmental stages, as in the Nelson lab microdissection work (Kerk et al. Plant Phys 132:27 2003), the Benfey lab root cell sorting experiments (e.g. Brady et al. Science 318:5851 2007), or our flower work, (e.g. Jiao and Meyerowitz Mol. Sys. Biol. 6, article 419, 2010), all of which isolate single cell type RNAs by very different methods.  The question of what we all mean by cell type is another issue...  Elliot

On Apr 9, 2013, at 1:07 AM, howie newick wrote:

>   Dear colleagues,
>   I was recently thinking about the active vs the inactive part of the
>   transcriptome. I would be very interested to get an idea of the
>   percentage of genes that is actually actively transcribed at any stage
>   of development. I could make an educated guess and speculate that
>   maybe 60-70% of the genes are being transcribed (on average), but has
>   this been ever quantified?
>   Although error-prone, one approach may be to look at microarray data
>   and use certain intensity cutoffs. But again, these cutoffs are
>   arbitrary ...
>   I would greatly appreciate ideas from the community.
>   Thank you very much in advance,
>   Howie
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