The Drosophila Histone Cluster is a gene cluster that contains more than a hundred copies of a sequence that encodes several histone proteins. These copies are very similar.

My question is what mechanism are known that could have played a role in the genesis of this cluster?

I'm aware of the possibility of recombination, which might expand the cluster on one chromosome, shortening it on the other. Are there any other mechanisms to expand or change the cluster and are there telltale signs left by these mechanisms in the genome sequence?

Given that in most species histone genes aren't clustered, it would be weird to assume that recombination is the only mechanism to duplicate these sequences. Also, at one end of the cluster bits and pieces of histone genes are mixed with other sequences, a bit like all the broken copies got pushed to one end. It would be interesting to have an explanation for this pattern.

  • $\begingroup$ Isn't this explained via gene duplication events? Or am I misunderstanding the question?en.wikipedia.org/wiki/… $\endgroup$
    – Ro Siv
    Commented Jul 28, 2015 at 22:02
  • $\begingroup$ Yes, but there are different gene duplication events. I already mentioned recombination. Is retrotransposition a possibility for histones? Can replications slippage account for 5000bp duplication? Or what is the max length for replication slippage? Is recombination the only mechanism that results in back to back copies? $\endgroup$ Commented Jul 29, 2015 at 7:33
  • $\begingroup$ It's an interesting question, though I don't think your claim that histone genes aren't clustered in most organisms is correct. On the contrary, both yeast and humans also have histone clusters. Given the evolutionary distance between these species, it would seem reasonable to expect that this phenomenon is quite ubiquitous. $\endgroup$
    – canadianer
    Commented Aug 4, 2015 at 7:57

1 Answer 1


This is the best review I have seen with a comprehensive discussion on gene duplication and amplification mechanisms (and it is also quite recent). It seems like there may be no definitive answers to your question in the literature--perhaps because of a paucity of viable experimental models that would allow one to test various hypotheses.

Also @canadianer is quite correct. Most metazoans with sequenced genomes have some kind of clustering of their histone genes (as well as multiple copies). In Drosophila embryogenesis the early zygotic cell-cycles are extraordinarily brief, on the order of 20 min as I recall, which means the fertilized egg is essentially a bag of DNA polymerase replication complexes. Therefore there is a very high demand for histone proteins. The gene amplification you describe is one way to achieve high concentrations of histones in a short time-frame.

Note that not all metazoans undergo this rapid burst of synchronous nuclear division, and therefore not all species have such a high copy number of core histone clusters.

  • $\begingroup$ Thank you, that is an interesting tidbit and what looks like a nice overview. I upvoted so you should get the bounty if nobody else comes along, even if I forget to accept the answer. But I'll probably do that later today anyway. $\endgroup$ Commented Aug 11, 2015 at 8:06

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