Comparative transcriptomics of primary cells in vertebrates.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
08
08
2019
accepted:
09
06
2020
pubmed:
29
7
2020
medline:
21
10
2021
entrez:
29
7
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32718981
pii: gr.255679.119
doi: 10.1101/gr.255679.119
pmc: PMC7397866
doi:
Substances chimiques
MicroRNAs
0
Transcription Factors
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
951-961Subventions
Organisme : Medical Research Council
ID : MC_UU_00007/11
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA200859
Pays : United States
Informations de copyright
© 2020 Alam et al.; Published by Cold Spring Harbor Laboratory Press.
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