Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

Scholes, Clarissa; Biette, Kelly M.; Harden, Timothy T.; DePace, Angela H.

doi:10.1016/j.celrep.2019.01.115

Cited by 41 publications

(50 citation statements)

References 60 publications

(127 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These concerns apply mostly to questions of the additivity of the Bra Proximal and Distal enhancers. Although they appear to be slightly super-additive in our experiments, this was not our major focus and a more elaborate set of controls akin to Scholes et al (2019) would be needed to fully explore this question. We have not, for example, excluded the possibility that the region between the Proximal and Distal enhancer elements might contain relevant transcription factor binding sites.…”

Section: Discussionmentioning

confidence: 92%

“…Distributed enhancer pairs have been found to function in sub-additive, additive and super-additive regimes (Bothma et al, 2015), although sub-additive and additive relationships have been most common in the limited number of cases where this has been addressed. Scholes et al (2019) recently found that the additivity of different combinations of Krüppel enhancers is not uniform as a function of the different concentrations of upstream activators present at different AP positions in the early Drosophila embryo. These particular enhancers are thought to respond to different combinations of upstream transcription factors, but it is also possible that distributed enhancers might have quantitatively different responses to the same upstream regulators.…”

Section: Introductionmentioning

confidence: 99%

“…A mechanistic understanding of how distributed enhancers work together to control gene expression depends on being able to quantify transcriptional input/output relationships in ways that are difficult in most model organisms. Quantitative analyses of distributed enhancer function have generally used the early Drosophila embryo as a model, where the AP patterning system provides natural gradients of key transcription factors (Perry et al, 2011, Bothma et al, 2015, El-Sherif and Levine, 2016, Park et al, 2019, Scholes et al, 2019. In most cases, however, the quantitative details of distributed enhancer function are completely unknown.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Harder

Hix

Reeves

et al. 2020

Preprint

View full text Add to dashboard Cite

Many genes are regulated by two or more enhancers that drive similar expression patterns. Evolutionary theory suggests that these seemingly redundant enhancers must have functionally important differences. In the simple ascidian chordate Ciona, the transcription factor Brachyury is induced exclusively in the presumptive notochord downstream of lineage specific regulators and FGF-responsive Ets family transcription factors. Here we exploit the ability to finely titrate FGF signaling activity via the MAPK pathway using the MEK inhibitor U0126 to quantify the dependence of transcription driven by different Brachyury reporter constructs on this direct upstream regulator. We find that the more powerful promoter-adjacent proximal enhancer and a weaker distal enhancer have fundamentally different dose-response relationships to MAPK inhibition. The Distal enhancer is more sensitive to MAPK inhibition but shows a less cooperative response, whereas the Proximal enhancer is less sensitive and more cooperative. A longer construct containing both enhancers has a complex dose-response curve that supports the idea that the proximal and distal enhancers are moderately super-additive. We show that the overall expression loss from intermediate doses of U0126 is not only a function of the fraction of cells expressing these reporters, but also involves graded decreases in expression at the single-cell level. Expression of the endogenous gene shows a comparable dose-response relationship to the full length reporter, and we find that different notochord founder cells are differentially sensitive to MAPK inhibition. Together, these results indicate that although the two Brachyury enhancers have qualitatively similar expression patterns, they respond to FGF in quantitatively different ways and act together to drive high levels of Brachyury expression with a characteristic input/output relationship. This indicates that they are fundamentally not redundant genetic elements.

show abstract

Section: Discussionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Harder

Hix

Reeves

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…This type of interaction is consistent with our finding that super-multiplicative gene expression responses are associated with nearby super-additive ATAC-seq peaks. Sub-additive transcriptional responses have been proposed to reflect saturation of cis-regulatory elements (Bothma et al, 2015;Scholes et al, 2019) . Saturated cis-regulatory elements would in principle show up as sub-additive ATAC-seq peaks in our analysis, but we did not observe an increase in sub-additive peaks near genes with sub-additive combined responses (with the exception of a small increase at high dose).…”

Section: Discussionmentioning

confidence: 99%

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

Sanford

Emert

Coté

et al. 2020

Preprint

View full text Add to dashboard Cite

Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-β), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined binding response was the sum of the binding responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.

show abstract

“…12enhancer-promoter loops(Furlong & Levine, 2018), recent studies suggest that enhancer-promoter 13 distance can indeed have an effect on expression levels(Carleton et al, 2017;Scholes et al, 2019). 14 Future studies will show whether the distance between enhancer and promoter can also affect the timing 15 of enhancer activity in a developmental setup.…”

mentioning

confidence: 99%

Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements

Thomas

Kotova

Pilz

et al. 2020

Preprint

View full text Add to dashboard Cite

14Many genes are regulated by multiple enhancers that often simultaneously activate their target gene. Yet, 15how individual enhancers collaborate to activate transcription is not well understood. Here, we dissect the 16 functions and interdependencies of five enhancer elements that form a previously identified enhancer 17 cluster and activate the Fgf5 locus during exit from naïve murine pluripotency. Four elements are located 18 downstream of the Fgf5 gene and form a super-enhancer. Each of these elements contributes to Fgf5 19 induction at a distinct time point of differentiation. The fifth element is located in the first intron of the 20 Fgf5 gene and contributes to Fgf5 expression at every time point by amplifying overall Fgf5 expression 21 levels. This amplifier element strongly accumulates paused RNA Polymerase II but does not give rise to a 22 mature Fgf5 mRNA. By transplanting the amplifier to a different genomic position, we demonstrate that it 23 enriches for high levels of paused RNA Polymerase II autonomously. Based on our data, we propose a 24 model for a mechanism by which RNA Polymerase II accumulation at a novel type of enhancer element, 25 the amplifier, contributes to enhancer collaboration. 26

show abstract

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

Cited by 41 publications

References 60 publications

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Ciona Brachyuryproximal and distal enhancers have different FGF dose-response relationships

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals

Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements

Contact Info

Product

Resources

About