Saturday, September 21, 2013

Journal club: sweet plots

This week's journal club paper is: Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana Stroud et al. (2012)

I thought it was very resourceful of Stroud et al. to pool together large datasets to make connections for H3.1 and H3.3 functional depositions. I have a couple of questions:

Is it possible that their use of H3.1/H3.3 Myc-tags transformed into the plant limits their ability to assay native H3.1/H3.3. So, maybe their absence of presence isn't necessarily evidence for absence? Is their concern for differential binding of the Myc-tags?

Frogee said that making Myc-tags is probably easier than finding specific antibodies for H3.1/H3.3. He's probably right, but I'm still curious how much more difficult making antibodies and if doing CHIP-seq with those antibodies would have yielded differences.

This is the first time I've encountered or maybe paid attention to plots that show values plotted against enrichment and distances from enrichment. I have no understanding of how this is done, but I think that I need to explore this technique of clustering these regions, because at least for me the figures look convincing. 

I'm curious as to how the H3.1 and H3.3 have been shown to evolve separately in plants and animals.

My comment:

This is the first time I've encountered plots that show values plotted against enrichment and distances from enrichment. I don't know how this technique of clustering these regions is done, but I want to find out, because, at least for me, the figures look like a convincing way to summarize data from many different regions of the genome.

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