Small DNA elements can act as both insulators and silencers in plants

Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of 8 large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of insulating or repressing transcription, depending on the regulatory context. We validate our findings in stable transgenic Arabidopsis thaliana, maize (Zea mays), and rice (Oryza sativa) plants. The short elements identified here should be useful building blocks for plant biotechnology.

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Publication Details

Journal
The Plant Cell
Published
2025-04-11
DOI
https://doi.org/10.1093/plcell/koaf084
Citations
6
Primary Topic
Plant Virus Research Studies
Type
article
Field-Weighted Citation Impact
10.50

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article

Small DNA elements can act as both insulators and silencers in plants

Jackson Tonnies, Shane Abbitt, Stanley Fields, Nagesh Sardesai et al.
6 citations
The Plant Cell
Plant Virus Research Studies
10.50
article

Small DNA elements can act as both insulators and silencers in plants

Jackson Tonnies, Shane Abbitt, Stanley Fields, Nagesh Sardesai, Christine Queitsch, Bing Yang, Josh T. Cuperus, Ajith Anand, William Gordon‐Kamm, Tobias Jores, Nicholas A. Mueth, Si Nian Char, Bo Liu, Stéphane Deschamps, Kathy Munkvold, Valentina Grillo-Alvarado, Scott Diehn, Heather Snowgren, Shuping Jiao
article en
6 citations

Abstract

Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments of 8 large insulators to identify more than 100 fragments that block enhancer activity. The short fragments can be combined to generate more powerful insulators that abolish the capacity of the strong viral 35S enhancer to activate the 35S minimal promoter. Unexpectedly, when tested upstream of weak enhancers, these fragments act as silencers and repress transcription. Thus, these elements are capable of insulating or repressing transcription, depending on the regulatory context. We validate our findings in stable transgenic Arabidopsis thaliana, maize (Zea mays), and rice (Oryza sativa) plants. The short elements identified here should be useful building blocks for plant biotechnology.

The Plant CellVol. 37(6)
University of Washington (US), Donald Danforth Plant Science Center (US), Corteva (United States) (US), Cluster of Excellence on Plant Sciences (DE), Brotman Baty Institute (US), Heinrich Heine University Düsseldorf (DE), University of Missouri (US)
U.S. Department of Agriculture, Deutsche Forschungsgemeinschaft, National Institutes of Health, National Science Foundation of Sri Lanka
Openalex Percentile: Top 2%
Plant Virus Research Studies
10.50
DOIOpen Access PDFOpenAlex
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