An RNA-Independent Linkage of Noncoding Transcription to Long-Range Enhancer Function

Abstract

The detection of noncoding transcription at multiple enhancers within the mammalian genome raises critical questions regarding whether and how this activity contributes to enhancer function. Here, using in vivo analysis of a human growth hormone (hGH) transgene locus, we report that activation of a domain of noncoding transcription adjacent to the long-range hGH-N enhancer, HSI, is established by the enhancer independent of any interactions with its target promoter. We further demonstrate that the appearance of this enhancer-linked noncoding transcription is temporally and spatially concordant with induction of hGH-N in the embryonic pituitary. Finally, we show that the level of transcriptional enhancement of hGH-N by HSI is directly related to the intensity of HSI-dependent noncoding transcription and is fully independent of the structure of the locally transcribed RNA. These data extend our understanding of the relationship of long-range enhancer activity to enhancer-dependent noncoding transcription and establish a model that may be of general relevance to additional mammalian loci.

ACKNOWLEDGMENTS

We thank the University of Pennsylvania Transgenic and Chimeric Mouse Facility (supported by National Institutes of Health [NIH] P30 grants DK019525, DK050306, and CA016520) for generation of the transgenic mice. We also thank Douglas Epstein, University of Pennsylvania, for critical review and comments, and Diane Dolson and Staci Rakowiecki for help with the in situ hybridization.

This study was supported by NIH grants R01 HD/DK25147 and R01 HD/DK046737 (to N.E.C. and S.A.L.).