Skip to main contentTools of the TradePublished: 10 November 2025Shaoqian Ma ORCID: orcid.org/0000-0001-8568-98521 Nature Reviews Genetics (2025)Cite this articleSubjectsGene expressionGene regulationRNA sequencingTranscriptionThe genome is decoded through transcription, which requires intricate interactions between DNA and proteins. Intriguingly, transcription is pervasive at the bulk level, yet less than 2% of the human genome encodes proteins. The exact fraction of the genome that is actively transcribed, and the extent to which noncoding transcription contributes to this activity within a single nucleus, remain unclear. A quantitative understanding of stochastic nascent transcription and its relevance to cell fate diversity and plasticity would substantially deepen our knowledge of how transient transcriptional dynamics coordinate robust gene regulatory outputs.Single-cell RNA sequencing offers unique advantages for dissecting cellular transcriptional heterogeneity. However, conventional approaches are dominated by mature mRNA signals and lack temporal resolution. Although metabolic labelling can introduce a temporal dimension, standard workflows often fail to capture short-lived RNAs on a genome-wide scale owing to extended labelling durations and poly(A)-based RNA enrichment.This is a preview of subscription content, access via your institutionAccess optionsAccess Nature and 54 other Nature Portfolio journalsGet Nature+, our best-value online-access subscription27,99 € / 30 dayscancel any timeLearn moreSubscribe to this journalReceive 12 print issues and online access269,00 € per yearonly 22,42 € per issueLearn moreBuy this articlePurchase on SpringerLinkInstant access to full article PDFBuy nowPrices may be subject to local taxes which are calculated during checkoutFig. 1: Overview of scFLUENT-seq.ReferencesOriginal articleMa, S. et al. Single-cell nascent transcription reveals sparse genome usage and plasticity. Cell https://doi.org/10.1016/j.cell.2025.09.003 (2025)Article PubMed PubMed Central Google Scholar Download referencesAuthor informationAuthors and AffiliationsSchool of Basic Medical Sciences, Tsinghua University, Beijing, ChinaShaoqian MaAuthorsShaoqian MaView author publicationsSearch author on:PubMed Google ScholarCorresponding authorCorrespondence to Shaoqian Ma.Ethics declarationsRights and permissionsReprints and permissionsAbout this article