Transposable element expression at unique loci in single cells with CELLO-seq

We introduce a novel method (CELLO-seq) for long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and Transposable Element (TE) expression at unique loci. We use CELLO-seq to assess the widespread expression of TEs in 2-cell mouse blastomeres as well as human induced pluripotent stem cells (hiPSCs). Across both species, old and young TEs showed evidence of locus-specific expression, with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed surprising heterogeneity, with TEs within a class showing different patterns of correlation, suggesting distinct regulatory mechanisms. CELLO-seq thus represents a significant advance in the research of TEs, highlighting that studying TEs in single cells and at single loci resolution is necessary for understanding how such elements are regulated and for gaining insight into their role during development.本研究提出一种全新的、可实现单细胞分辨率长读长RNA测序的方法（CELLO-seq）。CELLO-seq可实现全长RNA测序，并能够在特异性基因座上测定等位基因、转录本亚型以及转座因子（Transposable Element, TE）的表达量。本研究利用CELLO-seq，评估了2细胞期小鼠卵裂球以及人类诱导多能干细胞（human induced pluripotent stem cells, hiPSCs）中转座因子的广泛表达特征。在两个物种中，新旧转座因子均表现出基因座特异性表达的证据；模拟分析显示，小鼠中仅有极少数极年轻的转座因子无法被高置信度地比对定位。通过探究单个转座因子的表达与其推定调控因子之间的关联，研究团队发现了令人意外的异质性：同一类别下的转座因子展现出各异的相关性模式，这暗示其调控机制存在显著差异。因此，CELLO-seq为转座因子研究领域带来了重大进展，该研究凸显了在单细胞及单基因座分辨率下开展转座因子研究的必要性，这有助于理解此类因子的调控方式，并深入解析其在发育过程中的功能。