Comparative transcriptomics of primary cells in vertebrates

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Comparative transcriptomics of primary cells in vertebrates. / Alam, Tanvir; Agrawal, Saumya; Severin, Jessica; Young, Robert S.; Andersson, Robin; Arner, Erik; Hasegawa, Akira; Lizio, Marina; Ramilowski, Jordan A.; Abugessaisa, Imad; Ishizu, Yuri; Noma, Shohei; Tarui, Hiroshi; Taylor, Martin S.; Lassmann, Timo; Itoh, Masayoshi; Kasukawa, Takeya; Kawaji, Hideya; Marchionni, Luigi; Sheng, Guojun; Forrest, Alistair R. R.; Khachigian, Levon M.; Hayashizaki, Yoshihide; Carninci, Piero; de Hoon, Michiel J. L.

In: Genome Research, Vol. 30, No. 7, 2020, p. 951-961.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Alam, T, Agrawal, S, Severin, J, Young, RS, Andersson, R, Arner, E, Hasegawa, A, Lizio, M, Ramilowski, JA, Abugessaisa, I, Ishizu, Y, Noma, S, Tarui, H, Taylor, MS, Lassmann, T, Itoh, M, Kasukawa, T, Kawaji, H, Marchionni, L, Sheng, G, Forrest, ARR, Khachigian, LM, Hayashizaki, Y, Carninci, P & de Hoon, MJL 2020, 'Comparative transcriptomics of primary cells in vertebrates', Genome Research, vol. 30, no. 7, pp. 951-961. https://doi.org/10.1101/gr.255679.119

APA

Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., ... de Hoon, M. J. L. (2020). Comparative transcriptomics of primary cells in vertebrates. Genome Research, 30(7), 951-961. https://doi.org/10.1101/gr.255679.119

Vancouver

Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E et al. Comparative transcriptomics of primary cells in vertebrates. Genome Research. 2020;30(7):951-961. https://doi.org/10.1101/gr.255679.119

Author

Alam, Tanvir ; Agrawal, Saumya ; Severin, Jessica ; Young, Robert S. ; Andersson, Robin ; Arner, Erik ; Hasegawa, Akira ; Lizio, Marina ; Ramilowski, Jordan A. ; Abugessaisa, Imad ; Ishizu, Yuri ; Noma, Shohei ; Tarui, Hiroshi ; Taylor, Martin S. ; Lassmann, Timo ; Itoh, Masayoshi ; Kasukawa, Takeya ; Kawaji, Hideya ; Marchionni, Luigi ; Sheng, Guojun ; Forrest, Alistair R. R. ; Khachigian, Levon M. ; Hayashizaki, Yoshihide ; Carninci, Piero ; de Hoon, Michiel J. L. / Comparative transcriptomics of primary cells in vertebrates. In: Genome Research. 2020 ; Vol. 30, No. 7. pp. 951-961.

Bibtex

@article{19451d315e034be09ef8cb078980eb2b,
title = "Comparative transcriptomics of primary cells in vertebrates",
abstract = "Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.",
author = "Tanvir Alam and Saumya Agrawal and Jessica Severin and Young, {Robert S.} and Robin Andersson and Erik Arner and Akira Hasegawa and Marina Lizio and Ramilowski, {Jordan A.} and Imad Abugessaisa and Yuri Ishizu and Shohei Noma and Hiroshi Tarui and Taylor, {Martin S.} and Timo Lassmann and Masayoshi Itoh and Takeya Kasukawa and Hideya Kawaji and Luigi Marchionni and Guojun Sheng and Forrest, {Alistair R. R.} and Khachigian, {Levon M.} and Yoshihide Hayashizaki and Piero Carninci and {de Hoon}, {Michiel J. L.}",
note = "{\textcopyright} 2020 Alam et al.; Published by Cold Spring Harbor Laboratory Press.",
year = "2020",
doi = "10.1101/gr.255679.119",
language = "English",
volume = "30",
pages = "951--961",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "7",

}

RIS

TY - JOUR

T1 - Comparative transcriptomics of primary cells in vertebrates

AU - Alam, Tanvir

AU - Agrawal, Saumya

AU - Severin, Jessica

AU - Young, Robert S.

AU - Andersson, Robin

AU - Arner, Erik

AU - Hasegawa, Akira

AU - Lizio, Marina

AU - Ramilowski, Jordan A.

AU - Abugessaisa, Imad

AU - Ishizu, Yuri

AU - Noma, Shohei

AU - Tarui, Hiroshi

AU - Taylor, Martin S.

AU - Lassmann, Timo

AU - Itoh, Masayoshi

AU - Kasukawa, Takeya

AU - Kawaji, Hideya

AU - Marchionni, Luigi

AU - Sheng, Guojun

AU - Forrest, Alistair R. R.

AU - Khachigian, Levon M.

AU - Hayashizaki, Yoshihide

AU - Carninci, Piero

AU - de Hoon, Michiel J. L.

N1 - © 2020 Alam et al.; Published by Cold Spring Harbor Laboratory Press.

PY - 2020

Y1 - 2020

N2 - Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

AB - Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

U2 - 10.1101/gr.255679.119

DO - 10.1101/gr.255679.119

M3 - Journal article

C2 - 32718981

VL - 30

SP - 951

EP - 961

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 7

ER -

ID: 247073016