» Articles » PMID: 27863239

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Overview
Journal Cell
Publisher Cell Press
Specialty Cell Biology
Date 2016 Nov 19
PMID 27863239
Citations 476
Authors
Affiliations
Soon will be listed here.
Abstract

A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally precise gene-expression programs during development. Consequently, divergence in enhancer sequence and activity is thought to be an important mediator of inter- and intra-species phenotypic variation. Here, we give an overview of emerging principles of enhancer function, current models of enhancer architecture, genomic substrates from which enhancers emerge during evolution, and the influence of three-dimensional genome organization on long-range gene regulation. We discuss intricate relationships between distinct elements within complex regulatory landscapes and consider their potential impact on specificity and robustness of transcriptional regulation.

Citing Articles

In vivo deletion of a GWAS-identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in β-thalassemia.

Deleuze V, Stephen T, Salma M, Orfeo C, Jorna R, Maas A Sci Rep. 2025; 15(1):8996.

PMID: 40089598 DOI: 10.1038/s41598-025-94222-8.


Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.

Yang J, Zhou F, Luo X, Fang Y, Wang X, Liu X Cell Death Discov. 2025; 11(1):84.

PMID: 40032852 PMC: 11876437. DOI: 10.1038/s41420-025-02366-3.


Molecular mechanisms altering cell identity in cancer.

Zippo A, Beyes S Oncogene. 2025; .

PMID: 40011573 DOI: 10.1038/s41388-025-03314-2.


Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers.

Wang S, Wang Z, Zang C Nucleic Acids Res. 2025; 53(3).

PMID: 39868536 PMC: 11760973. DOI: 10.1093/nar/gkaf015.


The α-globin super-enhancer acts in an orientation-dependent manner.

Kassouf M, Francis H, Gosden M, Suciu M, Downes D, Harrold C Nat Commun. 2025; 16(1):1033.

PMID: 39863595 PMC: 11762767. DOI: 10.1038/s41467-025-56380-1.


References
1.
Kleinjan D, Bancewicz R, Gautier P, Dahm R, Schonthaler H, Damante G . Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PLoS Genet. 2008; 4(2):e29. PMC: 2242813. DOI: 10.1371/journal.pgen.0040029. View

2.
Whitaker J, Nguyen T, Zhu Y, Wildberg A, Wang W . Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods. 2014; 72:86-94. PMC: 4778972. DOI: 10.1016/j.ymeth.2014.10.008. View

3.
Tak Y, Farnham P . Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin. 2016; 8:57. PMC: 4696349. DOI: 10.1186/s13072-015-0050-4. View

4.
Zhu B, Zhang W, Zhang T, Liu B, Jiang J . Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures. Plant Cell. 2015; 27(9):2415-26. PMC: 4815101. DOI: 10.1105/tpc.15.00537. View

5.
Wittkopp P, Kalay G . Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet. 2011; 13(1):59-69. DOI: 10.1038/nrg3095. View