H3K4me3 and H3K27ac double peaks near TSS

Question

[tonja.r]

What is the reason of common double peaks near TSS of those two histone modifications: H3K4me3 and H3K27ac? They mark an active promoter in the promoter region but what do they do after TSS?

Answer 1

[Chirag Nepal]

Many genes have divergent transcripts in the antisense orientation. These divergent transcripts are quickly degraded. Double peaks at TSSs represent it's association with the gene and it's cognate RNA (divergent transcript). The dip between these two peaks represent nucleosome free region.

[tonja.r]

So, those peaks are not caused by the fact that polymerase might be sitting between them? Also, do you have some references that explain these effect? I have found lots of papers showing those double peaks but nobody explains the nature of it.

[Chirag Nepal]

Double peak defines the probable boundaries for regulatory elements. There are many reviews, i put one of the latest one. http://www.ncbi.nlm.nih.gov/pubmed/26317464

You can find many relevant papers in this review.

Answer 2

[abishai.dominic]

Hello !

To understand more on your answer. Are you trying to say that the region between the peaks, which is where there is a reduced H3k4me3, is a nucleosome free region ? Are you suggesting that most of the TSS regions associated with the H3K4me3 are nucleosome free ?

Please elaborate on this.

Thank you!

[Sinji]

Yes, in my experience with MNase-seq data and my research, it appears that the large majority of TSS regions (active at least, H3K27Ac+ and H3K4me3+) appear to be nucleosome free. This makes sense since you expect POLR2 binding.

[abishai.dominic]

So H3K4me3 should be lower in TSS sites, right?

Can you add some references to explain this more clearly?