Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.
Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes.
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DOI：
10.1038/s41587-023-01931-4
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发表时间：
2023-09
影响因子：
46.9
通讯作者：
Kunal Jindal;Mohd Tayyab Adil;Naoto Yamaguchi;Xue Yang;Helen C. Wang;Kenji Kamimoto;Guillermo C. Rivera-Gonza
中科院分区：
文献类型：
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作者：
Kunal Jindal;Mohd Tayyab Adil;Naoto Yamaguchi;Xue Yang;Helen C. Wang;Kenji Kamimoto;Guillermo C. Rivera-Gonza
复杂的基因调控机制是分化和重编程的基础。当代单细胞谱系追踪（scLT）方法使用表达的、可遗传的DNA条形码来将联合收割机细胞谱系读出与单细胞转录组学组合。然而，对转录谱的依赖限制了对其他单细胞测定的适应。使用CellTag-multi，我们提出了一种方法，该方法能够在单细胞RNA测序和使用测序测定的转座酶可降解染色质单细胞测定中直接捕获表达为聚腺苷酸化转录物的遗传随机条形码，从而允许转录和表观基因组细胞状态的独立克隆跟踪。我们验证CellTag-multi在小鼠造血过程中表征祖细胞谱系启动。此外，在成纤维细胞向内胚层祖细胞的直接重编程中，我们确定了靶向和脱靶命运的核心调控程序。此外，我们揭示了转录因子Zfp 281作为重编程结果的调节因子，使细胞偏向于脱靶间充质命运。我们的研究结果建立了CellTag-multi作为一种与多种单细胞模式兼容的谱系追踪方法，并证明了其在揭示不同分化和重编程范式中的命运指定基因调控变化方面的实用性。
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.