A single-cell transposable element atlas of human cell identity.

IF 4.3 Q1 BIOCHEMICAL RESEARCH METHODS

Cell Reports Methods Pub Date : 2025-06-18 DOI:10.1016/j.crmeth.2025.101086

Helena Reyes-Gopar, Jez L Marston, Bhavya Singh, Matthew Greenig, Jonah Lin, Mario A Ostrowski, Kipchoge N Randall, Santiago Sandoval-Motta, Nicholas Dopkins, Elsa Lawrence, Morgan M O'Mara, Tongyi Fei, Rodrigo R R Duarte, Timothy R Powell, Enrique Hernández-Lemus, Luis P Iñiguez, Douglas F Nixon, Matthew L Bendall

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Abstract

Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. The quantification of locus-specific TE expression in scRNA-seq experiments is challenging due to their repetitive sequence content and poorly characterized annotations. Here, we developed a computational tool for single-cell transposable element locus-level analysis of scRNA sequencing (Stellarscope) that reassigns multimapped reads to specific genomic loci using an expectation maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define cell subsets not identified by standard mRNA expression profiles. Altogether, this study provides comprehensive insights into the influence of TEs in human biology at the single-cell level.

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人类细胞身份的单细胞转座因子图谱。

单细胞RNA测序（scRNA-seq）正在彻底改变复杂生物系统的研究。然而，大多数测序研究忽略了转座因子（TE）表达对转录组的贡献。scRNA-seq实验中位点特异性TE表达的量化具有挑战性，因为它们的序列内容重复且特征注释不充分。在这里，我们开发了一种用于scRNA测序的单细胞转座元件位点水平分析的计算工具（stararscope），该工具使用期望最大化算法将多映射读段重新分配到特定的基因组位点。利用Stellarscope，我们构建了TE在人类PBMCs中的表达图谱。我们发现，基因座特异性te描述了细胞类型，并定义了标准mRNA表达谱无法识别的细胞亚群。总之，本研究在单细胞水平上对TEs对人类生物学的影响提供了全面的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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