Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom.
Norwich Medical School, The University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
Commun Biol. 2023 May 24;6(1):558. doi: 10.1038/s42003-023-04936-6.
Single-cell approaches have revealed that the haematopoietic hierarchy is a continuum of differentiation, from stem cell to committed progenitor, marked by changes in gene expression. However, many of these approaches neglect isoform-level information and thus do not capture the extent of alternative splicing within the system. Here, we present an integrated short- and long-read single-cell RNA-seq analysis of haematopoietic stem and progenitor cells. We demonstrate that over half of genes detected in standard short-read single-cell analyses are expressed as multiple, often functionally distinct, isoforms, including many transcription factors and key cytokine receptors. We observe global and HSC-specific changes in gene expression with ageing but limited impact of ageing on isoform usage. Integrating single-cell and cell-type-specific isoform landscape in haematopoiesis thus provides a new reference for comprehensive molecular profiling of heterogeneous tissues, as well as novel insights into transcriptional complexity, cell-type-specific splicing events and consequences of ageing.
单细胞方法揭示了造血层级是分化的连续体，从干细胞到定向祖细胞，其特征是基因表达的变化。然而，这些方法中的许多都忽略了异构体水平的信息，因此无法捕捉到系统内的选择性剪接的程度。在这里，我们对造血干细胞和祖细胞进行了短读长和长读长单细胞 RNA-seq 分析的整合。我们证明，在标准短读长单细胞分析中检测到的超过一半的基因都以多种、通常功能不同的异构体形式表达，包括许多转录因子和关键细胞因子受体。我们观察到随着年龄的增长，基因表达会发生全局和 HSC 特异性的变化，但年龄对异构体的使用影响有限。因此，整合单细胞和细胞类型特异性的异构体图谱在造血中提供了一个新的参考，用于对异质组织进行全面的分子分析，以及对转录复杂性、细胞类型特异性剪接事件和衰老后果的新见解。
