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As far as I know, chromatin consists of two kinds:

Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC.

Euchromatin is less condensed so translational factors have more access to this region, and this region is rich in GC.

I wonder how GC content affects the condensation status of the chromosome? What is the mechanism behind this relationship?

It is well known that GC and AT pairs differ in the number of their hydrogen bonds. Does this hydrogen bonding play the key role in condensation of chromosomes?

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@ThoH.Ho and @Thawn. When banding chromosomes they are first treated with trypsin before staining with Giemsa dye. My understanding, and I have worked in the field of cytogenetics for quite a while, is that chromatin condensation due to gene content IS the reason for differential banding patterns. Gene rich/ high GC content areas, with more open chromatin, are more readily digested by the trypsin enzyme and therefore less protein is then present to stain with Giemsa. Vice versa for the gene poor/ low GC content regions. This is why non coding regions such as heterochromatin stain very dark and gene rich chromosomes such as chromosome 19 are pale. So although chromosomes may be at their most condensed stage of the cell cycle in pro metaphase, there is obviously still a relative difference between chromatin condensation of the GC rich and GC poor regions.

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Chromosome condensation seems to be primarily driven by epigenetic factors like methylation and histone modifications, not GC content. However, high GC content is associated with gene rich regions and gene expression generally requires open chromatin. In other words high GC content correlates with genes, and genes being expressed correlate with open chromatin, so high GC content correlates with open chromatin, but isn't necessarily causal.

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    $\begingroup$ Thank you. I highly appreciate your point of view. There's only one thing, I'd like to hear your opinion on this, that the reason I asked this question is because of the G-banding. When people stain the chromosome using Giemsa solution, the cell is mostly in prometaphase or metaphase. Expression regulation should be very low at this stage, chromosomes should be condensed at a same level. So why they are stained differently while they are all condensed (metaphase)? $\endgroup$
    – Brainchild Ho
    Oct 15, 2017 at 7:02
  • $\begingroup$ @ThoH.Ho The question you ask in the comment is a completely different one from the question you originally posted. I suggest you ask a new question and specifically mention the giemsa stain. The dye used for the giemsa stain specifically binds to AT base pairs and this creates the banding. This has nothing to do with chromatin condensation. $\endgroup$
    – Thawn
    Mar 13, 2018 at 12:47

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