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Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms.

ABSTRACT: What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.

SUBMITTER: Crow M

PROVIDER: S-EPMC9071420 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms.

Crow Megan M Suresh Hamsini H Lee John J Gillis Jesse J

Nucleic acids research 20220501 8

What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-s ...[more]

PMID: 35451481

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