RT Journal
A1 Alam, Tanvir
A1 Agrawal, Saumya
A1 Severin, Jessica
A1 Young, Robert S.
A1 Andersson, Robin
A1 Arner, Erik
A1 Hasegawa, Akira
A1 Lizio, Marina
A1 Ramilowski, Jordan A.
A1 Abugessaisa, Imad
A1 Ishizu, Yuri
A1 Noma, Shohei
A1 Tarui, Hiroshi
A1 Taylor, Martin S.
A1 Lassmann, Timo
A1 Itoh, Masayoshi
A1 Kasukawa, Takeya
A1 Kawaji, Hideya
A1 Marchionni, Luigi
A1 Sheng, Guojun
A1 R.R. Forrest, Alistair
A1 Khachigian, Levon M.
A1 Hayashizaki, Yoshihide
A1 Carninci, Piero
A1 de Hoon, Michiel J.L.
T1 Comparative transcriptomics of primary cells in vertebrates
JF Genome Research 
JO Genome Research 
YR 2020 
FD July 01 
VO 30 
IS 7 
SP 951 
OP 961 
DO 10.1101/gr.255679.119 
UL http://genome.cshlp.org/content/30/7/951.abstract 
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.