CoChat
Sign Up
Cited by 293Genomics and Chromatin DynamicsChromosomal and Genetic VariationsCancer-related molecular mechanisms research

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Open access
Mikhaylichenko, Olga, Bondarenko, Vladyslav, Harnett, Dermot, Schor, Ignacio E., Males, Matilda, Viales, Rebecca R., Furlong, Eileen E.M.·2018·Genes & Development
DOI 10.1101/gad.308619.117PMC PMC5828394
Open this paper in CoChat — free accountOpen PDF

Abstract

Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/gad.308619.117

Cites

10 of 10 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The directionality of a regulatory element's transcriptional output is likely a key feature determining its position on the enhancer/promoter spectrum.

    “One key feature determining the position of a regulatory element on this spectrum is likely to be the directionality of its transcriptional output.”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [248]

  • In a Drosophila assay, unidirectionally transcribing elements were more likely to drive strong promoter and limited enhancer activity, whilst bi-directionally transcribing elements had strong potential for enhancer activity and could also function as weak promoters.

    “In a Drosophila assay, unidirectionally transcribing elements were more likely to drive strong promoter and limited enhancer activity, whilst bi-directionally transcribing elements had strong potential for enhancer activity and could also function as weak promoters [248].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [248]

  • Cis-regulatory elements exist on a spectrum of enhancer/promoter ability.

    “Recently, it has been proposed that cis-regulatory elements exist on a spectrum of enhancer/promoter ability [233, 248].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [248]

  • The level of eRNA transcription correlates with enhancer activity.

    “Several studies have shown that the level of eRNA transcription correlates with enhancer activity [60,61].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [61]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 69

  1. Almada AE, Wu X, Kriz AJ, Burge CB, Sharp PA. 2013 Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499: 360– 363. 23792564 PMC3720719
  2. Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A. 2014b Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun 5: 5336. 25387874
  3. Andersson R, Sandelin A, Danko CG. 2015 A unified architecture of transcriptional regulatory elements. Trends Genet 31: 426– 433. 26073855
  4. Archer TK, Lefebvre P, Wolford RG, Hager GL. 1992 Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255: 1573– 1576. 1347958
  5. Arenas-Mena C. 2017 The origins of developmental gene regulation. Evol Dev 19: 96– 107. 28116828
  6. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drablos F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, 2015 Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 347: 1010– 1014. 25678556 PMC4681433
  7. Arnold CD, Zabidi MA, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A. 2017 Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nat Biotechnol 35: 136– 144. 28024147 PMC5870828
  8. Bailey TL, Machanick P. 2012 Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 40: e128. 22610855 PMC3458523
  9. Banerji J, Rusconi S, Schaffner W. 1981 Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27: 299– 308. 6277502
  10. Barolo S, Carver LA, Posakony JW. 2000 GFP and β-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques 29: 726. 11056799
  11. Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. 2012 High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res 23: 169– 180. 22936248 PMC3530677
  12. Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS. 2005 Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci 102: 15907– 15911. 16249329 PMC1276093
  13. Bischof J, Maeda RK, Hediger M, Karch F, Basler K. 2007 An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci 104: 3312– 3317. 17360644 PMC1805588
  14. Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EEM. 2012a Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44: 148– 156. 22231485
  15. Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin A-C, Furlong EEM. 2012b Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7: 978– 994. 22538849
  16. Butler JE, Kadonaga JT. 2001 Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15: 2515– 2519. 11581157 PMC312797
  17. Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, 2017 Genetic variants regulating expression levels and isoform diversity during embryogenesis. Nature 541: 402– 406. 28024300
  18. Chen RAJ, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. 2013 The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res 23: 1339– 1347. 23550086 PMC3730107
  19. Cho H, Orphanides G, Sun X, Yang XJ, Ogryzko V, Lees E, Nakatani Y, Reinberg D. 1998 A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol 18: 5355– 5363. 9710619 PMC109120
  20. Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. 2012 Defining the status of RNA polymerase at promoters. Cell Rep 2: 1025– 1035. 23062713 PMC3483431
  21. Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. 2014 Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311– 1320. 25383968 PMC4254663
  22. Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, 2017 Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet 49: 1073– 1081. 28581502
  23. Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, 2017 A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods 14: 629– 635. 28417999 PMC5490986
  24. Duttke SHC, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. 2015 Human promoters are intrinsically directional. Mol Cell 57: 674– 684. 25639469 PMC4336624
  25. Fukaya T, Lim B, Levine M. 2016 Enhancer control of transcriptional bursting. Cell 166: 358– 368. 27293191 PMC4970759
  26. Gallo SM, Gerrard DT, Miner D, Simich M, Soye Des B, Bergman CM, Halfon MS. 2011 REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res 39: D118– D123. 20965965 PMC3013816
  27. Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. 2013 Enhancer transcripts mark active estrogen receptor binding sites. Genome Res 23: 1210– 1223. 23636943 PMC3730096
  28. Hebbar PB, Archer TK. 2008 Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA. J Biol Chem 283: 4595– 4601. 18156629 PMC3339569
  29. Ho Y, Elefant F, Liebhaber SA, Cooke NE. 2006 Locus control region transcription plays an active role in long-range gene activation. Mol Cell 23: 365– 375. 16885026
  30. Inoue F, Kircher M, Martin B, Cooper GM, Witten DM, McManus MT, Ahituv N, Shendure J. 2017 A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res 27: 38– 52. 27831498 PMC5204343
  31. Jeong S, Stein A. 1994 Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells. Nucleic Acids Res 22: 370– 375. 7510391 PMC523591
  32. Jiang J, Kosman D, Ip YT, Levine M. 1991 The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos. Genes Dev 5: 1881– 1891. 1655572
  33. Jin Y, Eser U, Struhl K, Churchman LS. 2017 The ground state and evolution of promoter region directionality. Cell 170: 889– 898.e10. 28803729 PMC5576552
  34. John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. 2011 Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264– 268. 21258342 PMC6386452
  35. Kim A, Zhao H, Ifrim I, Dean A. 2007 β-Globin intergenic transcription and histone acetylation dependent on an enhancer. Mol Cell Biol 27: 2980– 2986. 17283048 PMC1899946
  36. Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, la Chapelle de AL, Heidemann M, Hintermair C, 2011 Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 18: 956– 963. 21765417
  37. Kutach AK, Kadonaga JT. 2000 The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol Cell Biol 20: 4754– 4764. 10848601 PMC85905
  38. Kvon EZ, Kazmar T, Stampfel G, Yáñez-Cuna JO, Pagani M, Schernhuber K, Dickson BJ, Stark A. 2014 Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512: 91– 95. 24896182
  39. Kwak H, Fuda NJ, Core LJ, Lis JT. 2013 Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339: 950– 953. 23430654 PMC3974810
  40. Lam MTY, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, 2013 Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498: 511– 515. 23728303 PMC3839578
  41. Lam MTY, Li W, Rosenfeld MG, Glass CK. 2014 Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 39: 170– 182. 24674738 PMC4266492
  42. Lenhard B, Sandelin A, Carninci P. 2012 Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 13: 233– 245. 22392219
  43. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, 2012 Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148: 84– 98. 22265404 PMC3339270
  44. Li X-Y, Harrison MM, Villalta JE, Kaplan T, Eisen MB. 2014 Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. Elife 3: e03737. PMC4358338 25313869
  45. Lohmann I. 2003 Dissecting the regulation of the Drosophila cell death activator reaper. Gene Expr Patterns 3: 159– 163. 12711543
  46. Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT. 2016 Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 11: 1455– 1476. 27442863 PMC5502525
  47. Melgar MF, Collins FS, Sethupathy P. 2011 Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol 12: R113. 22082242 PMC3334599
  48. Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Vrielink JAFO, Elkon R, Melo SA, Léveillé N, Kalluri R, 2013 eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 49: 524– 535. 23273978
  49. Moreau P, Hen R, Wasylyk B, Everett R, Gaub MP, Chambon P. 1981 The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res 9: 6047– 6068. 6273820 PMC327583
  50. Natoli G, Andrau J-C. 2012 Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 46: 1– 19. 22905871
  51. Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM. 2016 High-throughput functional comparison of promoter and enhancer activities. Genome Res 26: 1023– 1033. 27311442 PMC4971761
  52. Ohler U. 2006 Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Res 34: 5943– 5950. 17068082 PMC1635271
  53. Plant KE, Routledge SJ, Proudfoot NJ. 2001 Intergenic transcription in the human β-globin gene cluster. Mol Cell Biol 21: 6507– 6514. 11533239 PMC99797
  54. Roy AL, Singer DS. 2015 Core promoters in transcription: old problem, new insights. Trends Biochem Sci 40: 165– 171. 25680757 PMC4340783
  55. Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, 2017 Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet 49: 550– 558. 28191888
  56. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, 2003 Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci 100: 15776– 15781. 14663149 PMC307644
  57. Sigova AA, Abraham BJ, Ji X, Molinie B, Hannett NM, Guo YE, Jangi M, Giallourakis CC, Sharp PA, Young RA. 2015 Transcription factor trapping by RNA in gene regulatory elements. Science 350: 978– 981. 26516199 PMC4720525
  58. Struhl K. 2007 Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14: 103– 105. 17277804
  59. Thomas S, Li X-Y, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, 2010 Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol 12: R43. PMC3219966 21569360
  60. Tuan D, Kong S, Hu K. 1992 Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc Natl Acad Sci 89: 11219– 11223. 1454801 PMC50521
  61. Vernimmen D. 2014 Uncovering enhancer functions using the α-globin locus. PLoS Genet 10: e1004668. 25330308 PMC4199490
  62. Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG, Higgs DR. 2007 Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J 26: 2041– 2051. 17380126 PMC1852780
  63. Vo Ngoc L, Wang Y-L, Kassavetis GA, Kadonaga JT. 2017 The punctilious RNA polymerase II core promoter. Genes Dev 31: 1289– 1301. 28808065 PMC5580651
  64. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, Zhou Y, Qiu J, Liu W, Kaikkonen MU, Ohgi KA, 2011 Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474: 390– 394. 21572438 PMC3117022
  65. Wilson CJ, Chao DM, Imbalzano AN, Schnitzler GR, Kingston RE, Young RA. 1996 RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 84: 235– 244. 8565069
  66. Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. 2014 Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet 10: e1004610. 25188404 PMC4154669
  67. Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, Liu J-L, Ponting CP. 2012 Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol 4: 427– 442. 22403033 PMC3342871
  68. Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A. 2015 Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518: 556– 559. 25517091 PMC6795551
  69. Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EEM. 2009 Combinatorial binding predicts spatio–temporal cis-regulatory activity. Nature 462: 65– 70. 19890324

Cited by

Sorted by citations

Authors
Mikhaylichenko, O., Bondarenko, V., Harnett, D., Schor, I. E., Males, M., Viales, R. R., & Furlong, E. E. M.
Affiliations
European Molecular Biology Laboratory (DE)
ORCID
Venue
Genes & Development
Publisher
Cold Spring Harbor Laboratory
Published
2018-01-01
Volume
32
Issue
1
Pages
42-57
ISSN
  • 0890-9369 (ISSN-L)
  • 1549-5477
DOI
10.1101/gad.308619.117
PMC
PMC5828394
OpenAlex
W2786141666
Cited by
293
References
10
Citations by year
2026: 19 · 2025: 24 · 2024: 46 · 2023: 34 · 2022: 31 · 2021: 47 · 2020: 39 · 2019: 26 · 2018: 27
Type
posted content
Language
en
Open access
Licence
cc-by
Locations
  • Genes & Development (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Americanae (AECID Library) (submittedVersion, cc-by-nc-sa)
  • HighWire Press Open Archive (submittedVersion)
  • LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-sa)
Funders
  • European Research Council (FP/2007-2013)
  • ERC (322851, CisRegVar)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Keywords
enhancer RNA, enhancer activity, promoter activity, bidirectional promoter, transcription directionality, Drosophila embryogenesis, developmental enhancers, enhancer function
MeSH terms
Animals, Drosophila, Enhancer Elements, Genetic, Humans, Promoter Regions, Genetic, Transcription, Genetic, Gene Expression Regulation, Developmental, K562 Cells, RNA, Untranslated, Embryonic Development

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review