Genome-Wide Analysis of mRNA Decay Rates and Their Determinants inArabidopsis thaliana

Abstract

To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to >24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 39 untranslated region are enriched among short-and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

“…Previous studies in Arabidopsis showed that transcripts of single-exon genes are relatively short-lived (Narsai et al, 2007). We observed that this also holds true for single-exon retrogenes and that retrogene intronization significantly increases their mRNA half-life.…”

“…We tested whether intronization plays a role in retrogene mRNA stability. First, we compared the mRNA half-life of transcribed retrogenes (n = 100), parents (n = 147), and the genome-wide set of transcribed genes (n = 13,012) included in the publicly available mRNA decay data set (Narsai et al, 2007). The mRNA half-life of the parents and the genomewide gene set was similar (MWW test, P = 0.21) and significantly longer than that of the retrogene mRNA (MWW test, P = 3.56 3 10 25 and P = 2.54 3 10 25 , respectively; Figure 2E).…”

“…The transcription borderline for transcribed genes (gcRMA $ 5) was based on the minimal density of genes between peaks indicating absent or background signals versus high transcription signals (Supplemental Figure 2). The Arabidopsis mRNA half-life data and rosette-and pollen-specific RNA sequencing data were extracted from previously published data sets (Narsai et al, 2007;Loraine et al, 2013). Randomized sets of genes or gene pairs were generated, plots drawn, and statistical tests calculated in R. The significance of density distributions was tested using the MWW rank-sum test with correction and cotranscription correlation by the Pearson productmoment correlation coefficient (r).…”

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

“…Major fluctuations in RNA stability are known to occur in plant regulatory responses to stress (Narsai et al. 2007). It may be that environmental stressors drive adaptation to the diverse habitats and seasonal extremes encompassed by this species' eastern North American range.…”

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

“…This is consistent with the role of these transcription factors as central regulators of anaerobic metabolism in rice. In terms of posttranscriptional regulation, it was observed that the transcripts of genes defined as aerobic contained five motifs enriched in the 3# UTR, one previously defined as a destabilization element (Narsai et al, 2007). Also, aerobic genes were significantly underrepresented in one element defined as a stabilization element (Narsai et al, 2007).…”