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

Crow, Megan, Suresh, Hamsini, Lee, John, Gillis, Jesse (April 2022) Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Research. ISSN 0305-1048

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DOI: 10.1093/nar/gkac276


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.

Item Type: Paper
Subjects: organism description > animal
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Gillis Lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 22 April 2022
Date Deposited: 02 May 2022 13:41
Last Modified: 09 May 2022 13:17
PMCID: PMC9071420

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