Im doing different analysis of the human chromosomes and diffent loci, however when using different databases, the heterochromatin structures are not part of the human genomes. I know that heterochromatin is a more dense structure within the DNA and stained differently and are not part of the different reference genomes.

However all the information regarding the human chromosome sizes, I can find all includes the heterochromatin regions.

So i would like to know, is there anywhere i can find the length of the human chromosomes without the heterochromatin structures?

Thanks for your time and help.


1 Answer 1


There are a couple of caveats that need to be addressed before answering this question:

  1. We don't know all of the regions in the human genome that can be heterochromatic. In some cases large chunks of heterochromatin are simply missing from the genome assembly. For a somewhat outdated but still informative review of the topic see here.
  2. Which regions are heterochromatic differs from cell to cell. For example, I would recommend reading about the differences between constitutive and facultative heterochromatin at wikipedia.
  3. Heterochromatic regions of the genome are very important biologically and not taking them into account could be a mistake, though it depends on your motivations.

The human genome project initially estimated that 92% of their original genome build is euchromatic, 2.85 Gbp total. However that original genome build has been substantially updated. That estimate is close enough for many purposes, probably. But we've learned a lot about genome structure and biology since that time.

We do have a lot of data that is highly correlated with what we think of as heterochromatin. The UCSC human genome browser has a lot of information about chromatin modifications (I would look at the ENCODE analysis section here). In principle you can make educated guesses about regions of heterochromatin based on chromatin modifications. This will be somewhat noisy, and you will have to make decisions about which cell types are relevant, as they will have somewhat different regions.

For more information about which chromatin modifications might be relevant, you might start looking here. You will likely need to analyze some data yourself to find a more precise answer.


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