Conservation of gene expression in vertebrate tissues

Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada.
Journal of Biology 05/2009; 8(3):33. DOI: 10.1186/jbiol130
Source: PubMed


Vertebrates share the same general body plan and organs, possess related sets of genes, and rely on similar physiological mechanisms, yet show great diversity in morphology, habitat and behavior. Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates.
We measured expression of all known and predicted genes across twenty tissues in chicken, frog and pufferfish. By combining the results with human and mouse data and considering only ten common tissues, we have found evidence of conserved expression for more than a third of unique orthologous genes. We find that, on average, transcription factor gene expression is neither more nor less conserved than that of other genes. Strikingly, conservation of expression correlates poorly with the amount of conserved nonexonic sequence, even using a sequence alignment technique that accounts for non-collinearity in conserved elements. Many genes show conserved human/fish expression despite having almost no nonexonic conserved primary sequence.
There are clearly strong evolutionary constraints on tissue-specific gene expression. A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis-regulatory restructuring.

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    • "conserved across distantly related species (Gasch et al. 2004; Chan et al. 2009). In comparison, studies of cis-regulatory sequences have shown that gain and loss of transcription factor binding sites is common (Moses et al. 2006; Doniger and Fay 2007; Kim et al. 2009; Bradley et al. 2010; Schmidt, et al. 2010; Yokoyama et al. 2014), and that between distantly related species, cis-regulatory sequences often diverge to the extent that the sequences are unalignable (Wratten et al 2006; Hare et al 2008; Venkatarum and Fay 2010; Arnold et al. 2014). "
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    • "We used high-throughput Illumina sequencing (RNA-seq) to identify transcribed genes in the endometrium during pregnancy in five Eutherian mammals (dog, cow, horse, pig, and armadillo), a marsupial (short-tailed opossum), and a Monotreme (platypus) and combined these data with existing gene expression data from the decidualized Rhesus monkey endometrium (Liu et al., 2012), decidualized mouse endometrium (McConaha et al., 2011), pregnant lizard uterus (Brandley et al., 2012), chicken uterus (Chan et al., 2010), and frog uterus (Chan et al., 2009). We also used RNA-seq to identify transcribed genes in human decidualized endometrial stromal cells (DSCs) in culture and combined these data with existing gene expression data from human decidual natural killer (dNK) cells (Hanna et al., 2006), decidual macrophage cells (dMP) (Svensson et al., 2011), and decidual endothelial cells (dECs). "
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    • "Comparative expression studies provide important insights into biological processes and can lead to the discovery of unknown regulation patterns. While evolutionary constraints on tissue-specific gene expression patterns have been extensively investigated [7-9,75,76], the constitutive regulation of RBP-mediated interactions is still poorly understood [11,12]. It has been previously observed that cellular localization and gene expression levels impose stringent conditions on the physicochemical properties of both protein and RNA sequences [77,78], but large-scale computational analyses of constitutive RBP-mediated regulatory networks have never been attempted before. "
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