Molecular competition can shape enhancer activity in the Drosophila embryo

Waymack, Rachel; Gad, Mario; Wunderlich, Zeba

doi:10.1016/j.isci.2021.103034

Cited by 9 publications

(9 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We acknowledge that thousands of genes are being transcribed in early embryos, and it is not intuitive to think that one additional transgene can affect the overall balance of TFs, Pol II, and PICs in each nucleus. Yet, others have reported similar phenomena of allelic competition, and we have also demonstrated that endogenous snail alleles interfere with each other ( Figure 4 ) ( Waymack et al, 2020 , 2021 ). While strong physical interactions between an enhancer and the target promoter often result in high transcriptional activity ( Symmons et al, 2016 ; Oudelaar et al, 2019 ), it was also demonstrated that the transcriptional efficiency is not linearly correlated with the degree of physical interactions ( Zuin et al, 2022 ).…”

Section: Discussionsupporting

confidence: 84%

“…One possible explanation is that transcription factors that are available to bind to enhancers are limiting. A recent study showed that a limiting number of transcription factors could lead to reduced RNA production from the homozygous allele ( Waymack et al, 2021 ). To further test this idea, we varied the strength of enhancer-promoter interactions without changing the enhancer sequence.…”

Section: Resultsmentioning

confidence: 99%

“…A recent study demonstrated a similar reduction of transcriptional activity in homozygotes compared to the hemizygotes, using reporter genes driven by the Krüppel enhancers. Inserting an array of Bcd or Zld TF binding sites on the homologous position was sufficient to reduce the transcriptional activity of the reporter gene, suggesting that the limiting number of TFs may induce allelic competition ( Waymack et al, 2021 ). This idea is in agreement with our finding that the stronger sna shadow enhancer exhibits allelic interference.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Shared Transcriptional Machinery at Homologous Alleles Leads to Reduced Transcription in Early Drosophila Embryos

Deng

Lim

2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

The mechanism by which transcriptional machinery is recruited to enhancers and promoters to regulate gene expression is one of the most challenging and extensively studied questions in modern biology. We explored the possibility that interallelic interactions between two homologous alleles might affect gene regulation. Using an MS2- and PP7-based, allele-specific live imaging assay, we visualized de novo transcripts of a reporter gene in hemizygous and homozygous Drosophila embryos. Surprisingly, each homozygous allele produced fewer RNAs than the corresponding hemizygous allele, suggesting the possibility of allelic competition in homozygotes. However, the competition was not observed when the enhancer-promoter interaction was weakened by placing the reporter construct in a different chromosome location or by moving the enhancer further away from the promoter. Moreover, the reporter gene showed reduced transcriptional activity when a partial transcription unit (either an enhancer or reporter gene only) was in the homologous position. We propose that the transcriptional machinery that binds both the enhancer and promoter regions, such as RNA Pol II or preinitiation complexes, may be responsible for the allelic competition. We showed that the degree of allelic interference increased over developmental time as more Pol II was needed to activate zygotic genes. Such allelic competition was observed for an endogenous gene as well. Our study provides new insights into the role of 3D interallelic interactions in gene regulation.

show abstract

Section: Discussionsupporting

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Shared Transcriptional Machinery at Homologous Alleles Leads to Reduced Transcription in Early Drosophila Embryos

Deng

Lim

2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

“…Instead, promoter competition might involve non-structural mechanisms whereby multiple promoters compete for rate-limiting factors (e.g. TFs, GTFs, RNA Pol2) present within shared transcriptional hubs 42,43,73 . Although these models and the putative rate-limiting factors await experimental validation, we speculate that nearby promoters with strong enhancer responsiveness and similar architecture (e.g.…”

Section: Discussionmentioning

confidence: 99%

Synergistic insulation of regulatory domains by developmental genes and clusters of CTCF sites

Ealo,

Sanchez-Gaya,

Respuela

et al. 2023

Preprint

View full text Add to dashboard Cite

The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow a certain level of physical crosstalk across regulatory domains, which is at odds with the highly specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites synergistically foster the robust insulation of regulatory domains. Firstly, we found that the TADs containing developmental genes have distinctive features, including the sequential organization of developmental genes and CTCF clusters near TAD boundaries. Most importantly, by genetically dissecting representative loci in mouse embryonic stem cells, we showed that developmental genes and CTCF sites synergistically strengthened the insulation capacity of nearby boundaries through different mechanisms. Namely, while CTCF sites prevent undesirable enhancer-gene contacts (i.e.physical insulation), developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the specificity of gene regulation, which in turn might help interpreting the pathological consequences of certain structural variants.

show abstract