One well-studied eRNA is the eRNA of the enhancer that interacts with the promoter of the prostate specific antigen (PSA) gene.  The PSA eRNA is strongly up-regulated by the androgen receptor.  High PSA eRNA then has a domino effect.  PSA eRNA binds to and activates the positive transcription elongation factor P-TEFb protein complex which can then phosphorylate RNA polymerase II (RNAP II), initiating its activity in producing mRNA.  P-TEFb can also phosphorylate the negative elongation factor NELF (which pauses RNAP II within 60 nucleotides after mRNA initiation begins).  Phosphorylated NELF is released from RNAP II, then allowing RNAP II to have productive mRNA progression (see Figure).  Up-regulated PSA eRNA thereby increases expression of 586 androgen receptor-responsive genes.  Knockdown of PSA eRNA or deleting a set of nucleotides from PSA eRNA causes decreased presence of phosphorylated (active) RNAP II at these genes causing their reduced transcription.
The negative elongation factor NELF protein can also be released from its interaction with RNAP II by direct interaction with some eRNAs. Schaukowitch et al. showed that the eRNAs of two immediate early genes (IEGs) directly interacted with the NELF protein to release NELF from the RNAP II paused at the promoters of these two genes, allowing these two genes to then be expressed.
In addition, eRNAs appear to interact with as many as 30 other proteins.