Karlsson Kasper, Linnarsson Sten
Departments of Medicine and Genetics, Stanford University, 94305, Stanford, CA, USA.
Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 1, SE-171 77, Stockholm, Sweden.
BMC Genomics. 2017 Feb 3;18(1):126. doi: 10.1186/s12864-017-3528-6.
Alternative mRNA isoform usage is an important source of protein diversity in mammalian cells. This phenomenon has been extensively studied in bulk tissues, however, it remains unclear how this diversity is reflected in single cells.
Here we use long-read sequencing technology combined with unique molecular identifiers (UMIs) to reveal patterns of alternative full-length isoform expression in single cells from the mouse brain. We found a surprising amount of isoform diversity, even after applying a conservative definition of what constitutes an isoform. Genes tend to have one or a few isoforms highly expressed and a larger number of isoforms expressed at a low level. However, for many genes, nearly every sequenced mRNA molecule was unique, and many events affected coding regions suggesting previously unknown protein diversity in single cells. Exon junctions in coding regions were less prone to splicing errors than those in non-coding regions, indicating purifying selection on splice donor and acceptor efficiency.
Our findings indicate that mRNA isoform diversity is an important source of biological variability also in single cells.
可变mRNA异构体的使用是哺乳动物细胞中蛋白质多样性的重要来源。这种现象已在大量组织中得到广泛研究，然而，目前尚不清楚这种多样性在单细胞中是如何体现的。
在这里，我们使用长读长测序技术结合独特分子标识符（UMIs）来揭示小鼠大脑单细胞中可变全长异构体的表达模式。我们发现了惊人数量的异构体多样性，即使在对什么构成异构体应用保守定义之后也是如此。基因倾向于有一个或几个高表达的异构体以及大量低水平表达的异构体。然而，对于许多基因，几乎每个测序的mRNA分子都是独特的，并且许多事件影响编码区域，这表明单细胞中存在以前未知的蛋白质多样性。编码区域的外显子连接比非编码区域的外显子连接更不容易发生剪接错误，这表明对剪接供体和受体效率存在纯化选择。
我们的研究结果表明，mRNA异构体多样性也是单细胞中生物变异性的重要来源。
