ArticlePlant biotechnology journal2022
Genome-wide prediction of activating regulatory elements in rice by combining STARR-seq with FACS.
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 18 citations in OpenAlex.
- Review
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- Modeling 0.6 million genes for the rational design of functionalProceedings of the National Academy of Sciences of the United States of America · 2024Article
- A high-efficient protoplast transient system for screening gene editing elements in Salvia miltiorrhiza.Plant cell reports · 2024Article
- Sea-ATI unravels novel vocabularies of plant active cistrome.Nucleic acids research · 2023Article
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- Mining theFrontiers in plant science · 2023Article
- A method for analyzing programmed cell death in xylem development by flow cytometry.Frontiers in plant science · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Self-transcribing active regulatory region sequencing (STARR-seq) is widely used to identify enhancers at the whole-genome level. However, whether STARR-seq works as efficiently in plants as in animal systems remains unclear. Here, we determined that the traditional STARR-seq method can be directly applied to rice (Oryza sativa) protoplasts to identify enhancers, though with limited efficiency. Intriguingly, we identified not only enhancers but also constitutive promoters with this technique. To increase the performance of STARR-seq in plants, we optimized two procedures. We coupled fluorescence activating cell sorting (FACS) with STARR-seq to alleviate the effect of background noise, and we minimized PCR cycles and retained duplicates during prediction, which significantly increased the positive rate for activating regulatory elements (AREs). Using this method, we determined that AREs are associated with AT-rich regions and are enriched for a motif that the AP2/ERF family can recognize. Based on GC content preferences, AREs are clustered into two groups corresponding to promoters and enhancers. Either AT- or GC-rich regions within AREs could boost transcription. Additionally, disruption of AREs resulted in abnormal expression of both proximal and distal genes, which suggests that STARR-seq-revealed elements function as enhancers in vivo. In summary, our work provides a promising method to identify AREs in plants.
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