Enhancer-derived RNA: A Primer

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2017 May 24

PMID 28533025

Citations 25

Authors

Feng Liu

Affiliations

Soon will be listed here.

Abstract

Enhancer-derived RNAs (eRNAs) are a group of RNAs transcribed by RNA polymerase II from the domain of transcription enhancers, a major type of cis-regulatory elements in the genome. The correlation between eRNA production and enhancer activity has stimulated studies on the potential role of eRNAs in transcriptional regulation. Additionally, eRNA has also served as a marker for global identification of enhancers. Here I review the brief history and fascinating properties of eRNAs.

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References

Levine M, Cattoglio C, Tjian R . Looping back to leap forward: transcription enters a new era. Cell. 2014; 157(1):13-25. PMC: 4059561. DOI: 10.1016/j.cell.2014.02.009. View

Murakawa Y, Yoshihara M, Kawaji H, Nishikawa M, Zayed H, Suzuki H . Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases. Trends Genet. 2016; 32(2):76-88. DOI: 10.1016/j.tig.2015.11.004. View

Shibayama Y, Fanucchi S, Mhlanga M . Visualization of Enhancer-Derived Noncoding RNA. Methods Mol Biol. 2016; 1468:19-32. DOI: 10.1007/978-1-4939-4035-6_3. View

Kaikkonen M, Spann N, Heinz S, Romanoski C, Allison K, Stender J . Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol Cell. 2013; 51(3):310-25. PMC: 3779836. DOI: 10.1016/j.molcel.2013.07.010. View

Lee T, Young R . Transcriptional regulation and its misregulation in disease. Cell. 2013; 152(6):1237-51. PMC: 3640494. DOI: 10.1016/j.cell.2013.02.014. View

Tuan D, Kong S, Hu K . Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc Natl Acad Sci U S A. 1992; 89(23):11219-23. PMC: 50521. DOI: 10.1073/pnas.89.23.11219. View

Roux B, Lindsay M, Heward J . Knockdown of Nuclear-Located Enhancer RNAs and Long ncRNAs Using Locked Nucleic Acid GapmeRs. Methods Mol Biol. 2016; 1468:11-8. DOI: 10.1007/978-1-4939-4035-6_2. View

Zhao J, Zhao Y, Wang L, Zhang J, Karnes R, Kohli M . Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer. Oncotarget. 2016; 7(25):38551-38565. PMC: 5122410. DOI: 10.18632/oncotarget.9535. View

Marchese D, Sanchez de Groot N, Gotor N, Livi C, Tartaglia G . Advances in the characterization of RNA-binding proteins. Wiley Interdiscip Rev RNA. 2016; 7(6):793-810. PMC: 5113702. DOI: 10.1002/wrna.1378. View

10.

Chiang H, Schoenfeld L, Ruby J, Auyeung V, Spies N, Baek D . Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 2010; 24(10):992-1009. PMC: 2867214. DOI: 10.1101/gad.1884710. View

11.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M . An atlas of active enhancers across human cell types and tissues. Nature. 2014; 507(7493):455-461. PMC: 5215096. DOI: 10.1038/nature12787. View

12.

He H, Li W, Wu D, Nagy R, Liyanarachchi S, Akagi K . Ultra-rare mutation in long-range enhancer predisposes to thyroid carcinoma with high penetrance. PLoS One. 2013; 8(5):e61920. PMC: 3653903. DOI: 10.1371/journal.pone.0061920. View

13.

Collis P, Antoniou M, Grosveld F . Definition of the minimal requirements within the human beta-globin gene and the dominant control region for high level expression. EMBO J. 1990; 9(1):233-40. PMC: 551652. DOI: 10.1002/j.1460-2075.1990.tb08100.x. View

14.

Lam M, Li W, Rosenfeld M, Glass C . Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci. 2014; 39(4):170-82. PMC: 4266492. DOI: 10.1016/j.tibs.2014.02.007. View

15.

. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012; 489(7414):57-74. PMC: 3439153. DOI: 10.1038/nature11247. View

16.

Badis G, Berger M, Philippakis A, Talukder S, Gehrke A, Jaeger S . Diversity and complexity in DNA recognition by transcription factors. Science. 2009; 324(5935):1720-3. PMC: 2905877. DOI: 10.1126/science.1162327. View

17.

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen A . Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013; 498(7455):516-20. PMC: 3718886. DOI: 10.1038/nature12210. View

18.

Magnuson B, Veloso A, Kirkconnell K, de Andrade Lima L, Paulsen M, Ljungman E . Identifying transcription start sites and active enhancer elements using BruUV-seq. Sci Rep. 2015; 5:17978. PMC: 4675984. DOI: 10.1038/srep17978. View

19.

Espinosa J . Revisiting lncRNAs: How Do You Know Yours Is Not an eRNA?. Mol Cell. 2016; 62(1):1-2. DOI: 10.1016/j.molcel.2016.03.022. View

20.

Kim T, Hemberg M, Gray J, Costa A, Bear D, Wu J . Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010; 465(7295):182-7. PMC: 3020079. DOI: 10.1038/nature09033. View