Abstract
Steady-state mRNA levels are tightly regulated through a combination of transcriptional and post-transcriptional control mechanisms. The discovery of cis-acting DNA elements that encode these control mechanisms is of high importance. We have investigated the influence of conserved non-coding sequences (CNSs), DNA patterns retained after an ancient whole genome duplication event, on the breadth of gene expression and the rates of mRNA decay in Arabidopsis thaliana. The absence of CNSs near α duplicate genes was associated with a decrease in breadth of gene expression and slower mRNA decay rates while the presence CNSs near α duplicates was associated with an increase in breadth of gene expression and faster mRNA decay rates. The observed difference in mRNA decay rate was fastest in genes with CNSs in both non-transcribed and transcribed regions, albeit through an unknown mechanism. This study supports the notion that some Arabidopsis CNSs regulate the steady-state mRNA levels through post-transcriptional control mechanisms and that CNSs also play a role in controlling the breadth of gene expression.
Highlights
Duplication of genetic material has been proposed to be one of the primary evolutionary factors driving organism complexity and occurs at various scales ranging from single gene transpositions to whole genome duplication (WGD) events (Freeling and Thomas, 2006; Edger and Pires, 2009; Freeling, 2009; Schnable et al, 2011; Woodhouse et al, 2011)
As average expression intensity (AEI) can vary based on coding sequences (CNSs) subgene position, we looked for a similar effect on the rate of mRNA decay by examining the half-lives of α duplicates with only non-transcribed CNSs, α duplicates with only transcribed CNSs, and α duplicates with both non-transcribed and transcribed CNSs
We suggest these differences in rates of mRNA decay are partially responsible for changes in breadth of gene expression (τ and coefficient of variation (CV))
Summary
Duplication of genetic material has been proposed to be one of the primary evolutionary factors driving organism complexity and occurs at various scales ranging from single gene transpositions to whole genome duplication (WGD) events (Freeling and Thomas, 2006; Edger and Pires, 2009; Freeling, 2009; Schnable et al, 2011; Woodhouse et al, 2011). The retention of specific functional classes encoded in duplicated genes suggests the fractionation process may involve a combination of factors including environmental cues, gene duplication scale (e.g., single gene transposition vs WGD), and relative levels of gene expression (Birchler et al, 2005; Zou et al, 2009; Wang et al, 2011; Yang and Gaut, 2011). Genes retained after a WGD event are thought to be retained more frequently relative to discrete duplication events as WGD events would copy all flanking DNA that encodes contains regulatory information (Schnable et al, 2011; Wang et al, 2011). Through the study of conserved non-coding DNA sequence flanking duplicated loci (CNS elements), it is possible to identify specific regulatory motifs copied and retained after the duplication event
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