ArticleScientific reports2021
Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
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Who cites it
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 64 citations in OpenAlex.
- Revealing the molecular landscape of human placenta: a systematic review and meta-analysis of single-cell RNA sequencing studies.Human reproduction update · 2024Pooled it
- Public Transcriptomic Data Meta-Analysis Demonstrates TAAR6 Expression in the Mental Disorder-Related Brain Areas in Human and Mouse Brain.Biomolecules · 2022Pooled it
- Temporal gating dictates stress-induced transcript export from the nucleus.Genes & development · 2026Article
- A cytoplasmic index for quantifying immune-related A-to-I RNA editing.Genome biology · 2026Article
- Temporal gating dictates stress-induced transcript export from the nucleus.bioRxiv : the preprint server for biology · 2026Article
- Persistent cortical excitatory neuron dysregulation in adultResearch square · 2025Article
- Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.Communications biology · 2025Article
- The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution.Nature cancer · 2025Article
- Article
- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Nuclei Isolation from Ocular Tissues of the Embryonic Chicken for Single-Nucleus Profiling.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Compartment-specific small non-coding RNA changes and nucleolar defects in human mesial temporal lobe epilepsy.Acta neuropathologica · 2024Article
- Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations.Plant communications · 2024Article
- Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase.American journal of physiology. Cell physiology · 2024Article
- Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes.bioRxiv : the preprint server for biology · 2024Article
- Regulatory function and mechanism research for m6A modification WTAP via SUCLG2-AS1- miR-17-5p-JAK1 axis in AML.BMC cancer · 2024Article
- LINC02086 promotes cell viability and inhibits cell apoptosis in breast cancer by sponging miR-6757-5p and up-regulating EPHA2.World journal of surgical oncology · 2023Article
- The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts.Nature protocols · 2023Review
- Transcriptional profiling of dental sensory and proprioceptive trigeminal neurons using single-cell RNA sequencing.International journal of oral science · 2023Article
- Cell-specific MAPT gene expression is preserved in neuronal and glial tau cytopathologies in progressive supranuclear palsy.Acta neuropathologica · 2023Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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