Agrawal Saumya, Kanamaru Emi, Saito Yoriko, Ishikawa Fumihiko, de Hoon Michiel
RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
NAR Genom Bioinform. 2025 Mar 7;7(1):lqaf007. doi: 10.1093/nargab/lqaf007. eCollection 2025 Mar.
Enhancers are noncoding regulatory regions in the genome that play essential roles in modulating gene expression. Previous work showed that enhancers are not transcriptionally silent but are characterized by bidirectional expression of short capped noncoding RNAs. Balanced bidirectional expression has therefore been used as a key feature for the detection of enhancers from transcriptome data. Instead, by analyzing FANTOM5 and other deep cap analysis gene expression transcriptome datasets, we find enhancer transcription preferentially in one direction in individual cell types. As the preferred direction of transcription of an enhancer can switch between cell types, balanced bidirectional enhancer expression may appear if transcriptome data are aggregated over cell types. 5' single-cell RNA sequencing data showed that enhancers were almost exclusively expressed unidirectionally in a single cell. Reporter assay data demonstrated that the regulatory function of an enhancer does not depend on its preference for unidirectional or bidirectional expression. We conclude that requiring balanced bidirectional transcription for enhancer detection may discard most valid enhancers when applied to transcriptome data of a single cell type.
增强子是基因组中的非编码调控区域，在调节基因表达中发挥着重要作用。先前的研究表明，增强子并非转录沉默，而是以短帽非编码RNA的双向表达为特征。因此，平衡的双向表达已被用作从转录组数据中检测增强子的关键特征。然而，通过分析FANTOM5和其他深度帽分析基因表达转录组数据集，我们发现在个体细胞类型中增强子转录优先在一个方向上。由于增强子转录的偏好方向可在细胞类型间切换，如果转录组数据是跨细胞类型汇总的，可能会出现平衡的双向增强子表达。5'单细胞RNA测序数据表明，增强子在单个细胞中几乎只单向表达。报告基因检测数据表明，增强子的调控功能并不取决于其对单向或双向表达的偏好。我们得出结论，当应用于单一细胞类型的转录组数据时，要求平衡的双向转录来检测增强子可能会遗漏大多数有效的增强子。
