Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of
Lhb
which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the
Lhb
locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates
Lhb
expression, following its splicing in situ. GnRH activates
Lhb
transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits
Lhb
, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and
Lhb
mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
Supplementary Information
The online version contains supplementary material available at 10.1007/s00018-024-05398-7.