H3k4me3 near TSS

Question

[abishai.dominic]

I am reading an article for my class presentation and have attached the pubmed link with this http://www.ncbi.nlm.nih.gov/pubmed/27292631

I have several questions on Fig 2A from the article, which is the global chip-seq data for H3K4me3 in the TSS. It would very helpful if someone elaborate on how they obtain the figure and what represents the x and y axis.

Also, there is a drop in the H3K4me3 at the TSS, which contradicts the fact that H3K4me3 is abundant near TSS and is a mark of active transcription. Why there is a lower methylation at the TSS and there is higher methylation at the upstream and the downstream of the TSS.

Thank you!

Answer 1

[Carlo Yague]

Since this is school work I'm not going to give a direct answer but I hope this will be useful.

Concerning fig2.A, you could look into the methods/code of Lovén et al., 2013 :

Material&Methods : Sequencing data from ChIP experiments was aligned to hg19 using Bowtie (Langmead et al., 2009). The mapBam.py script to map reads from a bam to a gff file was used to determine quantitative fold changes in H3K4me3 after MK treatment (Lovén et al., 2013)

If you don't find the info you are looking for then here is a little hint : this kind of figure is sometimes called metagene analysis.

Concerning your second question, I and others provided some possible explanations in another one of your post.

[abishai.dominic]

Thank you Carlo! My presentation was over last week :) I am curious to understand it better. I Will read and get back to you.

Thank you!