Gene-Rich And Gene-Poor Human Genomic Location

Question

[Shumon Shumon]

Hi,

I want to compare my ChIP-seq read distribution (Human, T47D cell line, hg18) in gene-rich and gene-poor region. What approach would be the best to define this location, or simply, from where I can get these gene-rich (or euchromatin) and gene-poor/gene-desert (heterochromatin) location bed file?

thanks,

Shumon

Answer 1

[Leonor Palmeira]

I think the chromatin picture is not as black and white as you describe it, and what you are looking for might not be available as a simple bed file.

The euchromatin/heterochromatin distinction comes from "ancient" times where this property was discovered by nuclear staining (heterochromatin is more packed and would appear darker than euchromatin).

Now, after this observation, people discovered some correlation between chromatin compaction and gene expression. Euchromatin being roughly the actively transcribed regions and heterochromatin being the silenced regions (either because they don't bear so many genes or because the genes are heavily methylated and silenced).

So, heterochromatin is in fact a mixture of at least two different things, what people now call "constitutive heterochromatin" (roughly centromeres, telomeres) and "facultative heterochromatin" (variable heterochromatin that can become euchromatin in other cell types, for instance).

I think what you should be looking for is data on chromatin compaction in your cell-type. A quick search on your cell-type gave me this paper, and this paper.