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Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

Zaghlool, Ammar, 1980- (author)
Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
Niazi, Adnan (author)
Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi
Björklund, Åsa K. (author)
Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab
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Orzechowski Westholm, Jakub (author)
Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Stockholm Univ, Natl Bioinformat Infrastruct Sweden, Dept Biochem & Biophys, Sci Life Lab, Box 1031, S-17121 Solna, Sweden
Ameur, Adam (author)
Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab
Feuk, Lars (author)
Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
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 (creator_code:org_t)
2021-02-18
2021
English.
In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Subject headings

NATURVETENSKAP  -- Biologi -- Cellbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Cell Biology (hsv//eng)
NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)
NATURVETENSKAP  -- Biologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

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