A unified architecture of transcriptional regulatory elements - PubMed (original) (raw)
Review
A unified architecture of transcriptional regulatory elements
Robin Andersson et al. Trends Genet. 2015 Aug.
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
Keywords: core promoter; eRNA; enhancer; promoter; transcriptional regulation.
Copyright © 2015 Elsevier Ltd. All rights reserved.
Similar articles
- Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities.
Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Rennie S, et al. Nucleic Acids Res. 2018 Jun 20;46(11):5455-5469. doi: 10.1093/nar/gky244. Nucleic Acids Res. 2018. PMID: 29659982 Free PMC article. - Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model.
Andersson R. Andersson R. Bioessays. 2015 Mar;37(3):314-23. doi: 10.1002/bies.201400162. Epub 2014 Dec 2. Bioessays. 2015. PMID: 25450156 Review. - Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN.
Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J. Zacher B, et al. PLoS One. 2017 Jan 5;12(1):e0169249. doi: 10.1371/journal.pone.0169249. eCollection 2017. PLoS One. 2017. PMID: 28056037 Free PMC article. - The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription.
Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. Mikhaylichenko O, et al. Genes Dev. 2018 Jan 1;32(1):42-57. doi: 10.1101/gad.308619.117. Epub 2018 Jan 29. Genes Dev. 2018. PMID: 29378788 Free PMC article. - Evaluating Enhancer Function and Transcription.
Field A, Adelman K. Field A, et al. Annu Rev Biochem. 2020 Jun 20;89:213-234. doi: 10.1146/annurev-biochem-011420-095916. Epub 2020 Mar 20. Annu Rev Biochem. 2020. PMID: 32197056 Review.
Cited by
- Nascent RNA analyses: tracking transcription and its regulation.
Wissink EM, Vihervaara A, Tippens ND, Lis JT. Wissink EM, et al. Nat Rev Genet. 2019 Dec;20(12):705-723. doi: 10.1038/s41576-019-0159-6. Epub 2019 Aug 9. Nat Rev Genet. 2019. PMID: 31399713 Free PMC article. Review. - An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping.
de Llobet Cucalon L, Di Vona C, Morselli M, Vezzoli M, Montanini B, Teichmann M, de la Luna S, Ferrari R. de Llobet Cucalon L, et al. Int J Mol Sci. 2022 Feb 18;23(4):2260. doi: 10.3390/ijms23042260. Int J Mol Sci. 2022. PMID: 35216376 Free PMC article. - Identification of regulatory elements from nascent transcription using dREG.
Wang Z, Chu T, Choate LA, Danko CG. Wang Z, et al. Genome Res. 2019 Feb;29(2):293-303. doi: 10.1101/gr.238279.118. Epub 2018 Dec 20. Genome Res. 2019. PMID: 30573452 Free PMC article. - Protein-Functionalized DNA Nanostructures as Tools to Control Transcription in Zebrafish Embryos.
Angelin A, Kassel O, Rastegar S, Strähle U, Niemeyer CM. Angelin A, et al. ChemistryOpen. 2016 Dec 28;6(1):33-39. doi: 10.1002/open.201600153. eCollection 2017 Feb. ChemistryOpen. 2016. PMID: 28168148 Free PMC article. - Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome.
Trinh LA, Chong-Morrison V, Gavriouchkina D, Hochgreb-Hägele T, Senanayake U, Fraser SE, Sauka-Spengler T. Trinh LA, et al. Cell Rep. 2017 Apr 11;19(2):425-440. doi: 10.1016/j.celrep.2017.03.045. Cell Rep. 2017. PMID: 28402863 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources