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

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...

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Autores principales:	Ammar Zaghlool, Adnan Niazi, Åsa K. Björklund, Jakub Orzechowski Westholm, Adam Ameur, Lars Feuk
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9a91b169ba164e37b3d0b15f348a8368
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spelling	oai:doaj.org-article:9a91b169ba164e37b3d0b15f348a83682021-12-02T14:03:57ZCharacterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts10.1038/s41598-021-83541-12045-2322https://doaj.org/article/9a91b169ba164e37b3d0b15f348a83682021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83541-1https://doaj.org/toc/2045-2322Abstract 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.Ammar ZaghloolAdnan NiaziÅsa K. BjörklundJakub Orzechowski WestholmAdam AmeurLars FeukNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ammar Zaghlool Adnan Niazi Åsa K. Björklund Jakub Orzechowski Westholm Adam Ameur Lars Feuk Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
description	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.
format	article
author	Ammar Zaghlool Adnan Niazi Åsa K. Björklund Jakub Orzechowski Westholm Adam Ameur Lars Feuk
author_facet	Ammar Zaghlool Adnan Niazi Åsa K. Björklund Jakub Orzechowski Westholm Adam Ameur Lars Feuk
author_sort	Ammar Zaghlool
title	Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
title_short	Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
title_full	Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
title_fullStr	Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
title_full_unstemmed	Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts
title_sort	characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of rna transcripts
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9a91b169ba164e37b3d0b15f348a8368
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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

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