The Epigenetics Revolution

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 head[135]. 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 2[136]. 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.

Here’s another surprising thing. Until very recently, all long ncRNAs were thought to repress gene expression. In 2010, Professor Ramin Shiekhattar at the Wistar Institute in Philadelphia identified over 3,000 long ncRNAs in a number of human cell types. These long ncRNAs showed different expression patterns in different human cell types, suggesting they had specific roles. Professor Shiekhattar and his colleagues tested a small number of the long ncRNAs to try to determine their functions. They used well-established experimental methods to knock down expression of their test ncRNAs and then analysed expression of their neighbouring genes. The predicted outcome, and the actual results, are shown in Figure 10.2.

^{Figure 10.2 ncRNAs were thought to repress expression of target genes. If this hypothesis were correct, then decreasing the expression of a specific ncRNA should result in more expression of the target gene, as the repression diminishes. This is shown in the middle panel. However, it is now becoming clear that a large number of ncRNAs actually drive up expression of their target genes. This has been shown by cases in which experimentally decreasing the expression of an ncRNA has the effect shown in the right hand side of this figure.}

Twelve ncRNAs were tested, and in seven cases the scientists found the result shown in the right-hand panel of Figure 10.2. This was contrary to expectations, because it suggests that about 50 per cent of long ncRNAs may actually increase expression of neighbouring genes, not decrease it[137].

Rather pithily, the authors of the paper stated, ‘The precise mechanism by which our ncRNAs function to enhance gene expression is not known.’ It’s a statement that is very hard to argue with. It has considerable merit as it makes clear that we currently have no idea how this is happening. Ramin Shiekhattar’s work does demonstrate rather convincingly that there is a lot we don’t understand about long ncRNAs, and that we should be wary of creating new dogma too quickly.

Small is beautiful

We should also be wary of assuming that size is everything and that big is best. The long ncRNAs clearly have major importance in cell function, but there is another equally importance class of ncRNAs that also has a significant impact in the cell. The ncRNAs in this class are short (usually 20–24 bases in length), and they target mRNA molecules, not DNA. This was first shown in our favourite worm, C. elegans.