Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo
Open accessAbstract
Metazoan genes are embedded in a rich milieu of regulatory information that often includes multiple enhancers possessing overlapping activities. In this study, we employ quantitative live imaging methods to assess the function of pairs of primary and shadow enhancers in the regulation of key patterning genes-knirps, hunchback, and snail-in developing Drosophila embryos. The knirps enhancers exhibit additive, sometimes even super-additive activities, consistent with classical gene fusion studies. In contrast, the hunchback enhancers function sub-additively in anterior regions containing saturating levels of the Bicoid activator, but function additively in regions where there are diminishing levels of the Bicoid gradient. Strikingly sub-additive behavior is also observed for snail, whereby removal of the proximal enhancer causes a significant increase in gene expression. Quantitative modeling of enhancer–promoter interactions suggests that weakly active enhancers function additively while strong enhancers behave sub-additively due to competition with the target promoter.
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A mixture of additive, synergistic and sub-additive effects was demonstrated in a live imaging analysis of candidate developmental enhancers in Drosophila embryos.
“a mixture of additive, synergistic and sub-additive effects was demonstrated in a live imaging analysis of candidate developmental enhancers in Drosophila embryos [519].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [519]
Some deviations from enhancer additivity could potentially be explained by steric constraints arising from enhancer competition or involvement of pioneer enhancers, but these considerations may not readily explain other reported cases.
“Some deviations from enhancer additivity could potentially be explained by steric constraints arising from enhancer competition [519] or involvement of “pioneer enhancers” [525], but these considerations may not readily explain other reported cases [523, 526].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [519]
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Cites
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125 · see citing works
Shadow enhancers as a source of evolutionary novelty
Hong, J.-W., Hendrix, D. A., & Levine, M. S. (2008) · Science · doi:10.1126/science.1160631 · Cited by 474 · see citing works
Self-citationHarrison, M. M., Li, X.-Y., Kaplan, T., Botchan, M. R., & Eisen, M. B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002266 · Cited by 338 · see citing works
Flagged first, then by citations
Research works printed but not linked: 26
- Bothma JP Garcia HG Esposito E Schlissel G Gregor T Levine M 2014 Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos Proceedings of the National Academy of Sciences of USA 7 1 6 10.1073/pnas.1410022111 PMC4115566 24994903 · DOI
- Buecker C Wysocka J 2012 Enhancers as information integration hubs in development: lessons from genomics Trends in Genetics 1 9 10.1016/j.tig.2012.02.008 PMC5064438 22487374 · DOI
- Di Talia S Wieschaus EF 2012 Short-term integration of Cdc25 dynamics controls mitotic entry during Drosophila gastrulation Developmental Cell 22 763 774 10.1016/j.devcel.2012.01.019 22483720 PMC3643212 · DOI
- Dunipace L Ozdemir A Stathopoulos A 2011 Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression Development 4084 4075 4084 10.1242/dev.069146 21813571 PMC3160101 · DOI
- Frankel N Davis GK Vargas D Wang S Payre F Stern DL 2010 Phenotypic robustness conferred by apparently redundant transcriptional enhancers Nature 466 490 493 10.1038/nature09158 20512118 PMC2909378 · DOI · Paper page
- Garcia HG Tikhonov M Lin A Gregor T 2013 Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning Current Biology 23 2140 2145 10.1016/j.cub.2013.08.054 24139738 PMC3828032 · DOI
- Gregor T Wieschaus EF Tank DW Bialek W 2007 Probing the limits to positional information Cell 130 153 164 10.1016/j.cell.2007.05.025 17632062 PMC2253670 · DOI
- Gregor T Garcia HG Little SC 2014 The embryo as a laboratory: quantifying transcription in Drosophila Trends in Genetics 30 364 375 10.1016/j.tig.2014.06.002 25005921 PMC4129518 · DOI
- Hocine S Raymond P Zenklusen D Chao JA Singer RH 2013 Single-molecule analysis of gene expression using two-color RNA labeling in live yeast Nature Methods 10 119 121 10.1038/nmeth.2305 23263691 PMC3899799 · DOI · Paper page
- Jeong Y El-Jaick K Roessler E Muenke M Epstein DJ 2006 A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers Development 133 761 772 10.1242/dev.02239 16407397 · DOI
- Kok K Arnosti DN 2015 Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors Frontiers in Genetics 6 29 10.3389/fgene.2015.00029 25713582 PMC4322839 · DOI
- Lagha M Bothma JP Levine M 2012 Mechanisms of transcriptional precision in animal development Trends in Genetics 28 1 8 10.1016/j.tig.2012.03.006 22513408 PMC4257495 · DOI
- Lam DD de Souza FS Nasif S Yamashita M López-Leal R Otero-Corchon V Meece K Sampath H Mercer AJ Wardlaw SL Rubinstein M Low MJ 2015 Partially redundant enhancers cooperatively naintain mammalian pomc expression above a critical functional threshold PLOS Genetics 11 1 21 10.1371/journal.pgen.1004935 PMC4335486 25671638 · DOI
- Levine M Cattoglio C Tjian R 2014 Looping back to leap forward: transcription enters a new era Cell 157 13 25 10.1016/j.cell.2014.02.009 24679523 PMC4059561 · DOI
- Levine M 2010 Transcriptional enhancers in animal development and evolution Current Biology 20 R754 R763 10.1016/j.cub.2010.06.070 20833320 PMC4280268 · DOI
- Little SC Tikhonov M Gregor T 2013 Precise developmental gene expression arises from globally stochastic transcriptional activity Cell 154 789 800 10.1016/j.cell.2013.07.025 23953111 PMC3778922 · DOI
- Liu F Morrison AH Gregor T 2013 Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network Proceedings of the National Academy of Sciences of USA 110 6724 6729 10.1073/pnas.1220912110 PMC3637740 23580621 · DOI
- Lucas T Ferraro T Roelens B De Las Heras Chanes J Walczak AM Coppey M Dostatni N 2013 Live imaging of bicoid-dependent transcription in Drosophila embryos Current Biology 23 2135 2139 10.1016/j.cub.2013.08.053 24139736 · DOI
- MacArthur S Li X-Y Li J Brown JB Chu HC Zeng L Grondona BP Hechmer A Simirenko L Keränen SV Knowles DW Stapleton M Bickel P Biggin MD Eisen MB 2009 Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions Genome Biology 10 R80 10.1186/gb-2009-10-7-r80 19627575 PMC2728534 · DOI
- Miller SW Rebeiz M Atanasov JE Posakony JW 2014 Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function Proceedings of the National Academy of Sciences of USA 111 17194 17199 10.1073/pnas.1415308111 PMC4260543 25404315 · DOI
- Nien C-Y Liang H-L Butcher S Sun Y Fu S Gocha T Kirov N Manak JR Rushlow C 2011 Temporal coordination of gene networks by Zelda in the early Drosophila embryo PLOS Genetics 7 e1002339 10.1371/journal.pgen.1002339 22028675 PMC3197689 · DOI
- Perry MW Boettiger AN Bothma JP Levine M 2010 Shadow enhancers foster robustness of Drosophila gastrulation Current Biology 20 1562 1567 10.1016/j.cub.2010.07.043 20797865 PMC4257487 · DOI · Paper page
- Perry MW Boettiger AN Levine M 2011 Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo Proceedings of the National Academy of Sciences of USA 108 13570 13575 10.1073/pnas.1109873108 PMC3158186 21825127 · DOI · Paper page
- Perry MW Bothma JP Luu RD Levine M 2012 Precision of hunchback expression in the Drosophila embryo Current Biology 22 2247 2252 10.1016/j.cub.2012.09.051 23122844 PMC4257490 · DOI
- Rushlow C Shvartsman SY 2012 Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient Current Opinion in Genetics & Development 22 542 546 10.1016/j.gde.2012.08.005 22981910 · DOI
- Venken KJT Carlson JW Schulze KL Pan H He Y Spokony R Wan KH Koriabine M de Jong PJ White KP Bellen HJ Hoskins RA 2009 Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster Nature Methods 6 431 434 10.1038/nmeth.1331 19465919 PMC2784134 · DOI
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Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161 · see citing works
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- Authors
- Bothma, J. P., Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., & Levine, M.
- Affiliations
- University of California, Berkeley (US)
- Department of Physics, Princeton University, Princeton, United States
- Princeton University (US)
- Corresponding author
- Gregor, Thomas
- Levine, Michael
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2015-08-12
- Volume
- 4
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC4532966
- OpenAlex
- W2123907240
- Cited by
- 192
- References
- 4
- Citations by year
- 2026: 14 · 2025: 27 · 2024: 14 · 2023: 18 · 2022: 14 · 2021: 27 · 2020: 15 · 2019: 14 · 2018: 17 · 2017: 16 · 2016: 14 · 2015: 2
- FWCI
- 7.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (NIH) (GM34431, GM071508, GM097275)
- Burroughs Wellcome Fund (101880)
- Physics Department, Princeton University (Dicke Fellowship)
- Searle Scholar Award (10-SSP-274)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- knirps, hunchback, snails, anterior-posterior patterning, enhancer-promoter interactions, gene fusion, Drosophila embryo, quantitative modeling
- MeSH terms
- Snail Family Transcription Factors, Animals, DNA-Binding Proteins, Drosophila, Enhancer Elements, Genetic, Evaluation Studies as Topic, Promoter Regions, Genetic, Repressor Proteins, Transcription Factors, Gene Expression Regulation, Developmental, Drosophila Proteins, Embryonic Development, Optical Imaging
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