Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus.
Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus.
复制标题
DOI：
10.1101/gr.262196.120
复制
发表时间：
2020-11
期刊：
影响因子：
7
通讯作者：
Gage FH
中科院分区：
文献类型：
--
作者：
Linker SB;Randolph-Moore L;Kottilil K;Qiu F;Jaeger BN;Barron J;Gage FH
目前，研究人员依赖于通用的方法来量化转座因子（TE）RNA表达，如RT-qPCR和RNA-seq，这些方法不能区分从自身启动子（真正的）表达的TE和从相邻基因启动子（如内含子或外显子）转录的TE。这种区别是重要的，因为TE的不同功能作用取决于它们是否独立转录。在这里，我们报告了一个简单的策略来检查真正的TE表达，称为BonaFide-TEseq。这种方法可以与任何基于模板转换的文库一起使用，例如Smart-seq 2或10 x的单细胞5′基因表达试剂盒，将其实用性扩展到单细胞RNA测序。这种方法不需要TE特异性富集，能够同时检测TE和蛋白质编码基因。我们发现，通过BonaFide-TEseq鉴定的TE是从它们自己的启动子表达的，而不是作为基因的内部产物被捕获。我们揭示了BonaFide-TEseq在单细胞数据分析中的实用性，并表明短散布核元件（西内斯）在小鼠海马中显示细胞类型特异性表达谱。我们进一步表明，在响应一个简短的家庭笼小鼠暴露于一种新的刺激，西内斯激活齿状颗粒神经元的时间过程中，是类似的蛋白质编码的立即早期基因。这项工作提供了一种简单的替代方法来评估真正的TE转录在单细胞分辨率，并提供了一个概念验证，使用这种方法来识别SINE激活的背景下，是相关的正常学习和记忆。
Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5′ gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type–specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
登录
查看更多内容
影响因子：
6.7
作者：
Karijolich J;Abernathy E;Glaunsinger BA
通讯作者：
Glaunsinger BA
影响因子：
64.5
作者：
Attig J;Agostini F;Gooding C;Chakrabarti AM;Singh A;Haberman N;Zagalak JA;Emmett W;Smith CWJ;Luscombe NM;Ule J
通讯作者：
Ule J
影响因子：
14.9
作者：
Belancio VP;Roy-Engel AM;Pochampally RR;Deininger P
通讯作者：
Deininger P
影响因子：
3.7
作者：
Kaer, Kristel;Branovets, Jelena;Speek, Mart
通讯作者：
Speek, Mart
DOI：
10.1073/pnas.0831042100
发表时间：
2003-04-29
影响因子：
11.1
作者：
Brouha, B;Schustak, J;Kazazian, HH
通讯作者：
Kazazian, HH