Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America.
PLoS One. 2011;6(8):e24251. doi: 10.1371/journal.pone.0024251. Epub 2011 Aug 29.
Genome-wide analysis has documented differential gene expression between closely related species in plants and animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, Arabidopsis thaliana and Arabidopsis arenosa, the majority of which are nonadditively expressed (differently from mid-parent value) in allotetraploids. Nonadditive gene expression can be caused by transcriptional regulation through chromatin modifications, but the role of posttranscriptional regulation in nonadditive gene expression is largely unknown. Here we reported genome-wide analysis of mRNA decay in resynthesized Arabidopsis allotetraploids. Among ∼26,000 annotated genes, over 1% of gene transcripts showed rapid decay with an estimated half-life of less than 60 minutes, and they are called allotetraploid genes with unstable transcripts (AlloGUTs). Remarkably, 30% of alloGUTs matched the nonadditively expressed genes, and their expression levels were negatively correlated with the decay rate. Compared to all genes, these nonadditively expressed alloGUTs were overrepresented 2-6-fold in the Gene Ontology (GOSlim) classifications in response to abiotic and biotic stresses, signal transduction, and transcription. Interestingly, the AlloGUTs include transcription factor genes that are highly inducible under stress conditions and circadian clock regulators that regulate growth in A. thaliana. These data suggest a role of mRNA stability in homoeologous gene expression in Arabidopsis allopolyploids. The enrichment of nonadditively expressed genes in stress-related pathways were commonly observed in Arabidopsis and other allopolyploids such as wheat and cotton, which may suggest a role for stress-mediated growth vigor in hybrids and allopolyploids.
全基因组分析记录了植物和动物中近缘物种之间的差异基因表达，以及与亲本相比杂种和异源多倍体中的非加性基因表达。在拟南芥中，相关物种拟南芥和拟南芥之间有 15-43%的基因表达不同，其中大多数在异源四倍体中表现出非加性表达（与中亲值不同）。非加性基因表达可能是由于染色质修饰的转录调控引起的，但在后转录调控中非加性基因表达的作用在很大程度上是未知的。在这里，我们报道了在重组合成的拟南芥异源四倍体中 mRNA 衰变的全基因组分析。在大约 26000 个注释基因中，超过 1%的基因转录本表现出快速衰变，半衰期不到 60 分钟，它们被称为不稳定转录物的异源四倍体基因（AlloGUTs）。值得注意的是，30%的 AlloGUTs 与非加性表达的基因匹配，其表达水平与衰变率呈负相关。与所有基因相比，这些非加性表达的 AlloGUTs 在生物和非生物胁迫、信号转导和转录等方面的基因本体论（GO Slim）分类中过度表达 2-6 倍。有趣的是，AlloGUTs 包括在胁迫条件下高度诱导的转录因子基因和调节拟南芥生长的生物钟调节器。这些数据表明，mRNA 稳定性在拟南芥异源多倍体中同源基因表达中起作用。在拟南芥和其他异源多倍体如小麦和棉花中，应激相关途径中非加性表达基因的富集是常见的，这可能表明应激介导的杂种和异源多倍体生长活力的作用。
