Abstract
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.
Highlights
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells
We argue that defining gene expression patterns at the subcellular level is crucial to (1) understand the differences between the cytosolic and nuclear transcriptomes and how each fraction contributes to the global gene expression patterns, (2) investigate the dynamics of subcellular RNA localization between different cells and different developmental stages as a regulatory mechanism to control protein expression and influence RNA function, and (3) evaluate the reliability of using nuclear transcriptome in single-cell studies as a proxy for whole-cell analysis
Our data provide the first resource for the subcellular localization of RNA transcript in the human brain
Summary
Transcriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis. Transcriptome analysis using RNA sequencing has primarily been performed on total or polyA + RNA from whole cells, overlooking the spatial dimension of gene expression at the subcellular level. Global profiling of the differences between nuclear and cytosolic fractions is crucial for accurately interpreting data from single-cell transcriptome studies. Understanding the main differences between the nuclear and cytosolic transcriptome in human tissues is important for meaningful interpretation of results from single-cell RNA sequencing experiments
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