Lineage tracing reveals hematopoietic stem cell (HSC) fates, while single-cell RNA sequencing identifies snapshots of HSC transcriptomes. To obtain information on fate plus transcriptome in the same cell, we developed the PolyloxExpress allele, enabling Cre-recombinase-dependent RNA barcoding in situ. Linking fates to single HSC transcriptomes provided the information required to identify transcriptional signatures of HSC fates, which were not apparent in single-HSC transcriptomes alone. We find that differentiation-inactive, multilineage, and lineage-restricted HSC clones reside in distinct regions of the transcriptional landscape of hematopoiesis. Differentiation-inactive HSC clones are closer to the origin of the transcriptional trajectory, yet they are not characterized by a quiescent gene signature. Fate-specific gene signatures imply coherence of clonal HSC fates, and HSC output toward short-lived lineage progenitors indicates stability of HSC fates over time. These combined analyses of fate and transcriptome under physiological conditions may pave the way toward identifying molecular determinants of HSC fates.

谱系追踪揭示了造血干细胞（HSC）的命运，而单细胞RNA测序可识别HSC转录组的快照。为了在同一细胞中获得关于命运和转录组的信息，我们开发了PolyloxExpress等位基因，可实现Cre重组酶依赖性RNA原位编码。将命运与单个HSC转录组联系起来提供了鉴定HSC命运的转录特征所需的信息，这在单独的单个HSC转录组中并不明显。我们发现分化非活性，多谱系和谱系限制的HSC克隆居住在造血细胞转录景观的不同区域。非分化非活性HSC克隆更接近转录轨迹的起源，但它们的特征不是静态基因签名。命运特定的基因特征暗示了克隆HSC命运的连贯性，向短命世系祖细胞输出的HSC随时间推移显示出HSC命运的稳定性。这些在生理条件下对命运和转录组的综合分析可能为鉴定HSC命运的分子决定因素铺平道路。