@article{4c9d108853094d0a970b182bd24172cd,
title = "Widespread transcription at neuronal activity-regulated enhancers",
abstract = "We used genome-wide sequencing methods to study stimulus-dependent enhancer function in mouse cortical neurons. We identified ∼12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. Notably, RNAPII at enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs) within enhancer domains defined by the presence of histone H3 monomethylated at lysine 4. The level of eRNA expression at neuronal enhancers positively correlates with the level of messenger RNA synthesis at nearby genes, suggesting that eRNA synthesis occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis. These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis.",
author = "Kim, {Tae Kyung} and Martin Hemberg and Gray, {Jesse M.} and Costa, {Allen M.} and Bear, {Daniel M.} and Jing Wu and Harmin, {David A.} and Mike Laptewicz and Kellie Barbara-Haley and Scott Kuersten and Eirene Markenscoff-Papadimitriou and Dietmar Kuhl and Haruhiko Bito and Worley, {Paul F.} and Gabriel Kreiman and Greenberg, {Michael E.}",
note = "Funding Information: Acknowledgements We thank members of the Greenberg laboratory for discussions and for critical reading of the manuscript. We thank S. Vasquez for preparing dissociated mouse cortical neurons. We thank L. Hu for generating antibodies. We thank the Molecular Genetics Core Facility at Children{\textquoteright}s Hospital Boston, including H. Schneider and S. Burgess, for operation of their SOLiD 3.0 sequencer (I.D.D.R.C). We thank the support and R&D teams at Life Technologies including S. Ranade, R. David, J. Ni, C. Barbacioru, M. Barker, G. Costa and K. McKernan. M.E.G. acknowledges the support of the Nancy Lurie Marks Family Foundation. We thank M. Dehoff for technical support in the Arc knockout experiments. This work was supported by the National Institutes of Health grants NS028829 (M.E.G.), R21EY019710 (G.K.), DP2OD006461 (G.K.) and MH-053608 (P.F.W.). This work was also supported by The Lefler postdoctoral fellowship (T-K.K.) and The Jane Coffin Childs Memorial Funds (T-K.K.), The Helen Hay Whitney postdoctoral fellowship (J.M.G.), The Children{\textquoteright}s Hospital Ophthalmology Foundation (G.K.), The Whitehall Foundation (G.K.), and The Klingenstein Fund (G.K.) Author Contributions T-K.K., J.M.G. and M.E.G. conceived and designed experiments. T-K.K., J.M.G., M.H., G.K. and M.E.G. wrote the manuscript. T-K.K. optimized the protocol for ChIP-Seq library preparation to be suitable for the SOLiD sequencer and made all ChIP-Seq libraries used in this study. S.K. invented the library construction methodology used for all RNA sequencing reported here. J.M.G., A.M.C. and E.M.-P. made all RNA-Seq libraries. M.H., J.M.G. and D.A.H. performed bioinformatic analyses. K.B.-H. carried out the SOLiD bead preparation and sequencing. T-K.K., J.W., P.F.W. and A.M.C. performed the Arc knockout experiment. D.M.B. performed the luciferase experiments. M.L. performed the RNA circularization experiment. H.B. provided the pArc7000 plasmid. D.K. provided the Arc knockout mouse. All authors reviewed the manuscript.",
year = "2010",
month = may,
day = "13",
doi = "10.1038/nature09033",
language = "English (US)",
volume = "465",
pages = "182--187",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7295",
}