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一个单细胞可转移的元素地图书的人类细胞身份

Helena Reyes-Gopar¹, Jez L Marston², Bhavya Singh³

¹Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX 04510, México; Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica, Ciudad de México CDMX 14610, México; Institute of Translational Research, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030, USA.

Cell reports methods

|June 21, 2025

概括

可转换元素 (TE) 的表达在生物学中至关重要. 我们的新工具Stellarscope分析了单细胞RNA测序 (scRNA-seq) 数据中的TE位点水平表达,揭示了以前通过标准分析隐藏的细胞类型和子集.

科学领域:

基因组学和分子生物学
计算生物学计算生物学
单细胞分析单细胞分析

背景情况:

单细胞RNA测序 (scRNA-seq) 是剖析生物复杂性的强大工具.
在scRNA-seq研究中,由于量化方面的挑战,可转移元素 (TE) 表达往往被忽视.
精确的特定位置的TE表达分析受到重复的序列和不完整的注释的阻碍.

研究的目的:

开发一种计算工具,用于对scRNA-seq数据中的可转换元素表达的位置层次分析.
在人体外周血液单核细胞 (PBMCs) 中创建TE表达图谱.
为了研究特定位置的TE表达在定义细胞类型和子集中的作用.

主要方法:

开发Stellarscope,这是一个用于单细胞可转移元素位置层次分析的计算工具.
利用预期最大化算法将多映射读数重新分配到特定的基因组位置.
应用了Stellarscope来分析人类PBMC中的TE表达.

主要成果:

恒星镜成功地从scRNA-seq数据中量化了特定位置的TE表达.
在人类PBMC中构建了TE表达的地图.
发现局部特异性TE可以划分不同的细胞类型,并定义以前未识别的细胞子集.

结论:

局部特定的可转移元素表达提供了对细胞异质性的新见解.
恒星镜是一种有效的工具,用于分析在scrRNA-seq.的位点水平上TE表达.
这项研究突出了TEs在单细胞水平上对人类生物学的重大影响.

关键词:

科普:遗传学遗传学 CP:系统生物学系统生物学星光望远镜 (Stellarscope) 是一个星光望远镜生物信息学是一种生物信息学.计算生物学是计算生物学.人类内源性逆转录病毒长时间间隔的核元素.机器学习是机器学习.逆转录组学 (retrotranscriptomics) 是一个学科.一个单细胞RNA测序.翻译学翻译学翻译学翻译学可转移的元素可以转移.

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