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Range extender mediates long-distance enhancer activity

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Bower, Grace, Hollingsworth, Ethan W., Jacinto, Sandra H., Alcantara, Joshua A., Clock, Benjamin, Cao, Kaitlyn, Liu, Mandy, Dziulko, Adam +9 more·2025·Nature
DOI 10.1038/s41586-025-09221-6PMC PMC12267059

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Abstract

Although most mammalian transcriptional enhancers regulate their cognate promoters over distances of tens of kilobases, some enhancers act over distances in the megabase range 1 . The sequence features that enable such long-distance enhancer–promoter interactions remain unclear. Here we used in vivo enhancer-replacement experiments at the mouse Shh locus to show that short- and medium-range limb enhancers cannot initiate gene expression at long-distance range. We identify a cis -acting element, range extender (REX), that confers long-distance regulatory activity and is located next to a long-range limb enhancer of Sall1 . The REX element has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range limb enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of REX increased the range of an enhancer by an order of magnitude from its native 73 kb to 848 kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs that are critical for its activity. These motifs are enriched in long-range limb enhancers genome-wide, including the ZRS (zone of polarizing activity (ZPA) regulatory sequence), a benchmark long-range limb enhancer of Shh 2 . The ZRS enhancer with mutated [C/T]AATTA motifs maintains limb activity at short range, but loses its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature associated with long-range enhancer–promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer long-distance activation by remote enhancers.

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  • The paper's observations expand the list of recently discovered long-range regulatory mechanisms that work by potentiating enhancer activity, such as facilitation and range extension.

    “Instead, our observations expand the list of recently discovered long-range regulatory mechanisms that work by potentiating enhancer activity, such as facilitation (60) and range extension (61).”

    From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [61]

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Authors
Bower, G., Hollingsworth, E. W., Jacinto, S. H., Alcantara, J. A., Clock, B., Cao, K., Liu, M., Dziulko, A., Alcaina-Caro, A., Xu, Q., Skowronska-Krawczyk, D., Lopez-Rios, J., Dickel, D. E., Bardet, A. F., Pennacchio, L. A., Visel, A., & Kvon, E. Z.
Affiliations
  • University of California, Irvine (US)
  • Lawrence Berkeley National Laboratory (US)
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
Kvon, Evgeny Z.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2025-07-02
Volume
643
Issue
8072
Pages
830-838
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-025-09221-6
PMC
PMC12267059
OpenAlex
W4411958289
Cited by
49
References
18
Citations by year
2026: 21 · 2025: 24 · 2024: 4
FWCI
12.38
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • HAL (submittedVersion, cc-by)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • U.S. Department of Energy
  • Ministerio de Ciencia e Innovación
  • National Institutes of Health (S10OD021718, 1s10rr025496-01, 1r01hd115268-01a1, S10OD010794)
  • University of California, Irvine
  • National Human Genome Research Institute (R01HG003988)
  • National Cancer Institute (P30CA062203)
  • National Institute of General Medical Sciences (T32GM008620, DP2GM149555)
  • National Institute of Neurological Disorders and Stroke (T32NS082174)
  • National Center for Research Resources (S10 RR025496)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01 HD115268, F30HD110233, F31HD112201)
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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
range extender, long-range enhancer-promoter interactions, SALL1, Sonic hedgehog, cis-regulatory elements, limb reduction, mouse development

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