ArticleGenome biology2025
Precise engineering of gene expression by editing plasticity.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Engineering climate-resilient horticultural crops: advances in transcriptional regulation, genome editing, and synthetic networks.Horticulture research · 2026Article
- PlantGFM: A Genomic Foundation Model for Discovery and Creation of Plant Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Reconfiguring biofortification strategies to transform food systems and address micronutrient deficiency of the 21st century.Journal of integrative plant biology · 2026Review
- A century of vitamin E research: The innovative journey from basic biology to synthetic bio-manufacturing.Journal of integrative plant biology · 2026Review
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Prime editing: a new frontier in precision genome engineering for rice improvement.Frontiers in plant science · 2026Review
- Rational design of promoter editing confers multipathogen resistance in rice.Genome biology · 2025Article
- DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning.Genome biology · 2025Article
- A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation.Frontiers in plant science · 2025Article
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Authors and funding
17 authors.
Funding
Abstract
backgroundIdentifying transcriptional cis-regulatory elements (CREs) and understanding their role in gene expression are essential for the precise manipulation of gene expression and associated phenotypes. This knowledge is fundamental for advancing genetic engineering and improving crop traits.
resultsWe here demonstrate that CREs can be accurately predicted and utilized to precisely regulate gene expression beyond the range of natural variation. We firstly build two sequence-to-expression deep learning models to respectively identify distal and proximal CREs by combining them with interpretability methods in multiple crops. A large number of distal CREs are verified for enhancer activity in vitro using UMI-STARR-seq on 12,000 synthesized sequences. These comprehensively characterized CREs and their precisely predicted effects further contribute to the design of in silico editing schemes for precise engineering of gene expression. We introduce a novel concept of "editingplasticity" to evaluate the potential of promoter editing to alter expression of each gene. As a proof of concept, both exhaustive prediction and random knockout mutants are analyzed within the promoter region of ZmVTE4, a key gene affecting α-tocopherol content in maize. A high degree of agreement between predicted and observed expression is observed, extending the range of natural variation and thereby allowing the creation of an optimal phenotype.
conclusionsOur study provides a robust computational framework that advances knowledge-guided gene editing for precise regulation of gene expression and crop improvement. By reliably predicting and validating CREs, we offer a tool for targeted genetic modifications, enhancing desirable traits in crops.
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