Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions

Kirthi Pulakanti, Luca Pinello, Cary Stelloh, Steven Blinka, Jeremy Allred, Samuel Milanovich, Sid Kiblawi, Jonathan Peterson, Alexander Wang, Guo Cheng Yuan, Sridhar Rao

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Enhancers are cis-acting elements capable of regulating transcription in a distance and orientation-independent manner. A subset of enhancers are occupied by RNA polymerase II (RNAP II) and transcribed to produce long non-coding RNAs termed eRNAs. We thoroughly investigated the association between eRNA productivity and various chromatin marks and transcriptional regulators in mouse embryonic stem cells (ESCs) through an integrative approach. We found that eRNA-producing enhancers exhibited elevated levels of the active mark H3K27Ac, decreased DNA methylation, and enrichment for the DNA hydroxylase Tet1. Many eRNA-producing enhancers have recently been characterized as "super-enhancers," suggesting an important role in the maintenance of pluripotency. Using experimental methods, we focally investigated a well-characterized enhancer linked to the Nanog locus and confirmed its exclusive eRNA productivity in ESCs. We further demonstrate that the binding of Sall4 and Tet family proteins were required for eRNA productivity at this locus. Collectively, we demonstrate that Tet1 binding and DNA hypomethylation are hallmarks of eRNA production.

Original languageEnglish (US)
Pages (from-to)1303-1320
Number of pages18
Issue number12
StatePublished - Oct 17 2013

Bibliographical note

Funding Information:
The authors would like to thank all the groups who placed their various datasets into the NCBI database, many of whom provided us with additional information and/or guidance with regards to analysis of their respective datasets. We would like to thank Dr Xiaochun Xu (Univ. of Michigan) for generously providing the anti-Tet2 antibody used in this work. This work is funded in part by NHLBI (HL087951 to Rao S) and NHGRI (HG005085 to Yuan G). In addition, Rao S is supported by a pilot grant from the American Cancer Society (Institutional Research Grant #86-004) and the Midwest Athletes against Childhood Cancer.

Copyright 2013 Elsevier B.V., All rights reserved.


  • DNA methylation
  • Enhancer Transcribed RNAs (eRNAs)
  • Non-coding RNA
  • Tet-proteins
  • Transcriptional enhancers


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