When a gene's promoter turns out to regulate its neighbour

Our paper on mechanisms for regulatory crosstalk between neighbouring genes is online in Nature. Some points to highlight.

Make heterozygous knockouts to study cis effects. That design is what lets you attribute an effect to the allele it happened on, rather than to the cell.

Many gene promoters regulate a neighbouring gene — 9 of the 18 we studied.

Most of these effects appear to be promoters acting either as enhancers or as competitive DNA repressors, rather than through the RNA they produce.

In one locus, the process of transcription and the 5′ splice site of the lncRNA are important — but not the specific sequence of the RNA. (Asked later why deleting an intron in Blustr upregulates Sfmbt2: our best guess is that it improves splicing and transcription. See supplementary note 6.)

We didn’t find any cis functions for 12 lncRNAs tested. Functional lncRNAs, or byproducts and transcriptional noise?

Read the paper in Nature.