近日，美国斯坦福大学医学院教授Jesse M. Engreitz及其团队的论文发现了重写调控DNA以解剖和重编程基因表达。这一研究成果于2025年4月16日发表在国际顶尖学术期刊《细胞》上。
该课题组研究人员利用CRISPR靶向筛选（variant - effects）从流分类实验中开发出变异效应，将数百种设计编辑引入内源性调节DNA，并量化它们对基因表达的影响。小组系统地解剖和重编程2种细胞类型的2个基因的3个调控元件。这些数据揭示了内源性因子结合位点对基因组环境具有特异性作用，转录因子基序具有细胞类型特异性活性，以及预测变异效应大小的计算模型的局限性。该课题组人员发现了可以在大动态范围内调节基因表达的小编辑，这为靶向调控DNA的基于引物编辑的治疗提供了新的可能性。Variant-EFFECTS提供了一种通用的工具来解剖调控DNA，并鉴定在内源性环境中调节基因表达的基因组编辑试剂。
研究人员表示，调控DNA为转录因子结合提供了一个平台，以编码细胞类型特异性的基因表达模式。然而，调控DNA序列的作用和可编程性仍然难以绘制或预测。
附：英文原文
Title: Rewriting regulatory DNA to dissect and reprogram gene expression
Author: Gabriella E. Martyn, Michael T. Montgomery, Hank Jones, Katherine Guo, Benjamin R. Doughty, Johannes Linder, Deepa Bisht, Fan Xia, Xiangmeng S. Cai, Ziwei Chen, Kelly Cochran, Kathryn A. Lawrence, Glen Munson, Anusri Pampari, Charles P. Fulco, Nidhi Sahni, David R. Kelley, Eric S. Lander, Anshul Kundaje, Jesse M. Engreitz
Issue&Volume: 2025-04-16
Abstract: Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context.
DOI: 10.1016/j.cell.2025.03.034
Source: https://www.cell.com/cell/abstract/S0092-8674(25)00352-6