Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

Pervouchine, Dmitri, Djebali, Sarah, Breschi, Alessandra, Davis, Carrie, Prieto Barja, Pablo, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael, Notredame, Cedric, Guigo, Roderic, Gingeras, Thomas (October 2014) Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes. BioRxiv. (Unpublished)

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Abstract

We characterized by RNA-seq the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles obtained in human cell lines reveals substantial conservation of transcriptional programs, and uncovers a distinct class of genes with levels of expression across cell types and species, that have been constrained early in vertebrate evolution. This core set of genes capture a substantial and constant fraction of the transcriptional output of mammalian cells, and participates in basic functional and structural housekeeping processes common to all cell types. Perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer. Evolutionary constraint in gene expression levels is not reflected in the conservation of the genomic sequences, but is associated with strong and conserved epigenetic marking, as well as to a characteristic post-transcriptional regulatory program in which sub-cellular localization and alternative splicing play comparatively large roles.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
organism description > animal > mammal > rodent > mouse
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Dobin Lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 30 October 2014
Date Deposited: 03 Jun 2021 20:02
Last Modified: 03 Jun 2021 20:02
URI: https://repository.cshl.edu/id/eprint/40197

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