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Estrogen receptor-α (ER)-positive breast cancer cells undergo hormone-independent proliferation after deprivation of oestrogen, leading to endocrine therapy resistance. Up-regulation of the ER gene ( ESR1 ) is critical for this process, but the underlying mechanisms remain unclear. Here we show that the combination of transcriptome and fluorescence  in situ  hybridization analyses revealed that oestrogen deprivation induced a cluster of noncoding RNAs that defined a large chromatin domain containing the  ESR1  locus. We termed these RNAs as  Eleanors  (ESR1 locus enhancing and activating noncoding RNAs).  Eleanors  were present in ER-positive breast cancer tissues and localized at the transcriptionally active  ESR1  locus to form RNA foci. Depletion of one  Eleanor ,  upstream  ( u)-Eleanor , impaired cell growth and transcription of intragenic  Eleanors  and  ESR1  mRNA, indicating that  Eleanors cis- activate the  ESR1  gene.  Eleanor -mediated gene activation represents a new type of locus control mechanism and plays an essential role in the adaptation of breast cancer cells.

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation