Yang Qiu, Lifen Liu, Jiali Yan, Xianglei Xiang, Shouzhe Wang et al.
Background: Identifying 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. Results: We 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. Conclusions: Our 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.
Yang Qiu, Lifen Liu, Jiali Yan, Xianglei Xiang, Shouzhe Wang, Yun Luo, Kaixuan Deng, Jieting Xu, Minliang Jin, Xiaoyu Wu, Liwei Cheng, Ying Zhou, Weibo Xie, Hai-Jun Liu, Alisdair R. Fernie, Xuehai Hu, Jianbing Yan. Precise engineering of gene expression by editing plasticity. 2025-03-10. https://doi.org/10.1186/s13059-025-03516-7
A synthetic library of 12,000 candidate 200-bp cis-regulatory elements was cloned into an episomal STARR-seq reporter and transiently transfected into maize leaf protoplasts. Four biological replicates were sequenced as cDNA and plasmid-input libraries; forward and reverse insert orientations were analyzed independently with DESeq2 RNA/input activity scores.
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