Context-dependent Enhancer Function Revealed by Targeted Inter-TAD Relocation

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Jun 17

PMID 35715427

Authors

Christopher Chase Bolt

Lucille Lopez-Delisle

Aurelie Hintermann

Benedicte Mascrez

Antonella Rauseo

Guillaume Andrey

Denis Duboule

Affiliations

Soon will be listed here.

Abstract

The expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.

Citing Articles

Genetic coupling of enhancer activity and connectivity in gene expression control.

Ray-Jones H, Sung C, Chan L, Haglund A, Artemov P, Della Rosa M Nat Commun. 2025; 16(1):970.

PMID: 39870618 PMC: 11772589. DOI: 10.1038/s41467-025-55900-3.

Biology of Hox Genes: Questions and Technological Challenges.

Parambil S, De Kumar B Methods Mol Biol. 2025; 2889:1-10.

PMID: 39745601 DOI: 10.1007/978-1-0716-4322-8_1.

CTCF-dependent insulation of and the heterochronic control of tail length.

Lopez-Delisle L, Zakany J, Bochaton C, Osteil P, Mayran A, Darbellay F Proc Natl Acad Sci U S A. 2024; 121(46):e2414865121.

PMID: 39499640 PMC: 11573545. DOI: 10.1073/pnas.2414865121.

Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.

Gobel A, Zhou S, Wang Z, Tzourtzou S, Himmelbach A, Zheng S Nat Commun. 2024; 15(1):9308.

PMID: 39468060 PMC: 11519323. DOI: 10.1038/s41467-024-53760-x.

CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant.

Kaplan S, Wong W, Yan J, Pulecio J, Cho H, Li Q Cell Rep. 2024; 43(8):114640.

PMID: 39163202 PMC: 11406439. DOI: 10.1016/j.celrep.2024.114640.

References

Woltering J, Vonk F, Muller H, Bardine N, Tuduce I, de Bakker M . Axial patterning in snakes and caecilians: evidence for an alternative interpretation of the Hox code. Dev Biol. 2009; 332(1):82-9. DOI: 10.1016/j.ydbio.2009.04.031. View

Oudelaar A, Beagrie R, Kassouf M, Higgs D . The mouse alpha-globin cluster: a paradigm for studying genome regulation and organization. Curr Opin Genet Dev. 2020; 67:18-24. PMC: 8100094. DOI: 10.1016/j.gde.2020.10.003. View

Woltering J, Irisarri I, Ericsson R, Joss J, Sordino P, Meyer A . Sarcopterygian fin ontogeny elucidates the origin of hands with digits. Sci Adv. 2020; 6(34):eabc3510. PMC: 7438105. DOI: 10.1126/sciadv.abc3510. View

Carroll S, Prudhomme B, Gompel N . Regulating evolution. Sci Am. 2008; 298(5):60-7. DOI: 10.1038/scientificamerican0508-60. View

Banerji J, Rusconi S, Schaffner W . Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell. 1981; 27(2 Pt 1):299-308. DOI: 10.1016/0092-8674(81)90413-x. View

Andrey G, Montavon T, Mascrez B, Gonzalez F, Noordermeer D, Leleu M . A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science. 2013; 340(6137):1234167. DOI: 10.1126/science.1234167. View

Lettice L, Heaney S, Purdie L, Li L, de Beer P, Oostra B . A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 2003; 12(14):1725-35. DOI: 10.1093/hmg/ddg180. View

Schaffner W . Enhancers, enhancers - from their discovery to today's universe of transcription enhancers. Biol Chem. 2015; 396(4):311-27. DOI: 10.1515/hsz-2014-0303. View

Dixon J, Selvaraj S, Yue F, Kim A, Li Y, Shen Y . Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485(7398):376-80. PMC: 3356448. DOI: 10.1038/nature11082. View

10.

Sheth R, Barozzi I, Langlais D, Osterwalder M, Nemec S, Carlson H . Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13. Cell Rep. 2016; 17(11):2913-2926. PMC: 5697718. DOI: 10.1016/j.celrep.2016.11.039. View

11.

Wolff P, Weinhofer I, Seguin J, Roszak P, Beisel C, Donoghue M . High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis Endosperm. PLoS Genet. 2011; 7(6):e1002126. PMC: 3116908. DOI: 10.1371/journal.pgen.1002126. View

12.

Woltering J, Noordermeer D, Leleu M, Duboule D . Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits. PLoS Biol. 2014; 12(1):e1001773. PMC: 3897358. DOI: 10.1371/journal.pbio.1001773. View

13.

Skene P, Henikoff J, Henikoff S . Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018; 13(5):1006-1019. DOI: 10.1038/nprot.2018.015. View

14.

Vieux-Rochas M, Fabre P, Leleu M, Duboule D, Noordermeer D . Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc Natl Acad Sci U S A. 2015; 112(15):4672-7. PMC: 4403207. DOI: 10.1073/pnas.1504783112. View

15.

Wolff J, Rabbani L, Gilsbach R, Richard G, Manke T, Backofen R . Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. Nucleic Acids Res. 2020; 48(W1):W177-W184. PMC: 7319437. DOI: 10.1093/nar/gkaa220. View

16.

Gilpatrick T, Lee I, Graham J, Raimondeau E, Bowen R, Heron A . Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol. 2020; 38(4):433-438. PMC: 7145730. DOI: 10.1038/s41587-020-0407-5. View

17.

Amandio A, Beccari L, Lopez-Delisle L, Mascrez B, Zakany J, Gitto S . Sequential in mutagenesis in vivo reveals various functions for CTCF sites at the mouse cluster. Genes Dev. 2021; 35(21-22):1490-1509. PMC: 8559674. DOI: 10.1101/gad.348934.121. View

18.

Osterwalder M, Barozzi I, Tissieres V, Fukuda-Yuzawa Y, Mannion B, Afzal S . Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018; 554(7691):239-243. PMC: 5808607. DOI: 10.1038/nature25461. View

19.

Grosveld F, van Staalduinen J, Stadhouders R . Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms. Annu Rev Genomics Hum Genet. 2021; 22:127-146. DOI: 10.1146/annurev-genom-122220-093818. View

20.

Ramirez F, Ryan D, Gruning B, Bhardwaj V, Kilpert F, Richter A . deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016; 44(W1):W160-5. PMC: 4987876. DOI: 10.1093/nar/gkw257. View