How does noncoding transcription regulate Hox genes?

Noncoding RNA has arrived at centre stage in recent years with the discovery of hidden transcriptomes in many higher organisms. Over two decades ago, noncoding transcripts were discovered in Drosophila Hox complexes but their function has remained elusive. Recent studies((1-3)) have examined the role of these noncoding RNAs in Hox gene regulation, and have generated a fierce debate as to whether the noncoding transcripts are important for silencing or activation. Here we review the evidence, and show that, by taking developmental timing into account, some of these apparently conflicting results can be resolved. We examine current models that explain these data and explore alternative interpretations.