Assigning Histone modification to TSSs based on Chip-seq

Question

[Zakaria Benmounah]

Hello,

While reading a scientific research paper, I confronted the following paragraph "We assigned histone modification to each of the protein-coding start site (29,000 protein coding start sites are identified from ENSEMBL) based on ChIPSeq data for the H1 ES cells. Each TSS was assigned a positive label for a given histone mark if a ChIPSeq peak was detected within 100 bp; if not, it was assigned a negative label."

I'm wondering how could we assign a histone modification mark to a Tss?

Best,

Answer 1

[biostart]

I understand that they do a peak calling, then search for ChIP-seq peaks within 100 bp near TSS. If a peak isfound, the TSS is assigned a mark "1", and if the peak is not found, the TSS is assigned a mark "0" (or whatever mark you want to assign).

[Zakaria Benmounah]

Indeed, I could add :

High levels of H3K4me1, H3K4me2, and H3K4me3 are detected surrounding transcription start sites (TSSs), whereas H3K36me3 peaks near the 3' end of genes

(High-Resolution Profiling of Histone Methylations in the Human Genome, Artem Barski et al., 2007)

that's why in the study they've been looking for histone modification near the transcription start site (TSS).

[Angle45]

Can you explain what this means (I'm a beginner in this field)? I don't understand why it is important to find histone methylations near TSS regions (what this means biologically)...

[Zakaria Benmounah]

It's known in epigenetics that histone modifications (methylation, acetylation,...) could play the role of both activating or repressing gene expression near the modified histone.

The key idea behind detecting which histone modification is near the TSS is to say that:

this X gene is activated by this M modification of this H histone. (assigning which gene could be activated by which modification of histone)