美国加州大学Nadav Ahituv团队近期取得重要工作进展，他们对转录调控元件进行了大规模平行表征。相关研究成果2025年1月15日在线发表于《自然》杂志上。

据介绍，人类基因组包含数百万个候选顺式调控元件（cCRE），这些元件具有细胞类型特异性活性，对健康及多种疾病状态都有影响。然而，人们对控制这些cCRE活性及细胞类型特异性的序列特征，在功能层面上仍缺乏了解。

研究人员利用基于慢病毒的大规模平行报告基因检测（lentiMPRA），对68万多个序列的调控活性进行了测试，这些序列广泛涵盖了三种细胞类型（HepG2、K562和WTC11）中注释的cCRE，结果发现其中41.7%的序列具有活性。通过对正反两个方向的序列进行测试，研究人员发现启动子存在链方向偏好，其中200个核苷酸的核心区域可作为非细胞类型特异性的“启动开关”，为相关基因提供相似的表达水平。

相比之下，增强子的方向偏好较弱，但组织特异性特征更强。利用lentiMPRA数据，研究人员开发了基于序列的模型，以高精度预测cCRE的功能和变异效应，描绘调控基序并模拟它们的组合效应。在这三种细胞类型中对包含6万个cCRE的lentiMPRA文库进行测试，进一步确定了决定细胞类型特异性的因素。

总之，这一研究提供了一份广泛的、针对三种常用细胞系的功能性CRE目录，并展示了如何利用大规模功能测定来剖析调控规则。

附：英文原文

Title: Massively parallel characterization of transcriptional regulatory elements

Author: Agarwal, Vikram, Inoue, Fumitaka, Schubach, Max, Penzar, Dmitry, Martin, Beth K., Dash, Pyaree Mohan, Keukeleire, Pia, Zhang, Zicong, Sohota, Ajuni, Zhao, Jingjing, Georgakopoulos-Soares, Ilias, Noble, William S., Yardmc, Galip Grkan, Kulakovskiy, Ivan V., Kircher, Martin, Shendure, Jay, Ahituv, Nadav

Issue&Volume: 2025-01-15

Abstract: The human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific activities that shape both health and many disease states1. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these cCREs. Here we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of more than 680,000 sequences, representing an extensive set of annotated cCREs among three cell types (HepG2, K562 and WTC11), and found that 41.7% of these sequences were active. By testing sequences in both orientations, we find promoters to have strand-orientation biases and their 200-nucleotide cores to function as non-cell-type-specific ‘on switches’ that provide similar expression levels to their associated gene. By contrast, enhancers have weaker orientation biases, but increased tissue-specific characteristics. Utilizing our lentiMPRA data, we develop sequence-based models to predict cCRE function and variant effects with high accuracy, delineate regulatory motifs and model their combinatorial effects. Testing a lentiMPRA library encompassing 60,000 cCREs in all three cell types further identified factors that determine cell-type specificity. Collectively, our work provides an extensive catalogue of functional CREs in three widely used cell lines and showcases how large-scale functional measurements can be used to dissect regulatory grammar.

DOI: 10.1038/s41586-024-08430-9

Source:https://www.nature.com/articles/s41586-024-08430-9