Transvection and pairing of a Drosophila Hox long noncoding RNA in the regulation of Sex combs reduced

Abstract

Long noncoding RNAs have emerged as abundant and important regulators of gene expression in diverse animals. In D. melanogaster several lncRNAs involved in regulating Hox gene expression in the Bithorax Complex have been reported. However, no functional Hox long noncoding RNAs have been described in the Antennapedia Complex. Here we have characterized a long noncoding RNA lincX from the Antennapedia Complex, that is transcribed from previously identified cis-regulatory sequences of the Hox gene Sex combs reduced (Scr). We use both the GAL4-UAS system and mutants to ectopically overexpress the lincX RNA from exogenous and endogenous loci respectively, in order to dissect the potential regulatory functions of lincX RNA versus lincX transcription. Our findings suggest that transcription through the lincX locus, but not the lincX RNA itself, may facilitate initiation of Scr in cis in the early embryo. Transvection phenomena, where regulatory sequences on one chromosome can affect expression on the homolog, have previously been reported in genetic studies of Scr. By analysing lincX and Scr nascent transcriptional sites in embryos heterozygous for a gain of function mutation, we directly visualize this transvection, and observe that the ectopic lincX transcriptional state appears to be relayed in trans to the homologous wild-type chromosome. This trans-activation of lincX correlates with both ectopic activation of Scr in cis, and increased chromosomal proximity. Our results are consistent with a model whereby early long noncoding RNA transcription through cis-regulatory sequences can be communicated between chromosomes, and facilitates long-range initiation of Hox gene expression in cis.