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There’s an amazing family of genes, called HOX genes. When they’re mutated in fruit flies (Drosophila melanogaster) the results are incredible phenotypes, such as legs growing out of the head14. There’s a long ncRNA known as HOTAIR, which regulates a region of genes called the HOX-D cluster. Just like the long ncRNAs investigated by Jeannie Lee, HOTAIR binds the PRC2 complex and creates a chromatin region which is marked with repressive histone modifications. But HOTAIR is not transcribed from the HOX-D position on chromosome 12. Instead it is encoded at a different cluster of genes called HOX-C on chromosome 215. No-one knows how or why HOTAIR binds at the HOX-D position. There’s a related mystery around the best studied of all long ncRNAs, Xist. Xist ncRNA spreads out along almost the entire inactive X chromosome but we really don’t know how. Chromosomes don’t normally become smothered with RNA molecules. There’s no obvious reason why Xist RNA should be able to bind like this, but we know it’s nothing to do with the sequence of the chromosome. The experiments described in the last chapter, where Xist could inactivate an entire autosome as long as it contained an X inactivation centre, showed that Xist just keeps on travelling once it’s on a chromosome. Scientists are basically still completely baffled about these fundamental characteristics of this best-studied of all ncRNAs.
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Nessa Carey (The Epigenetics Revolution: How Modern Biology is Rewriting our Understanding of Genetics, Disease and Inheritance)