Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses.
Unstable transcripts in Arabidopsis allotetraploids are associated with nonadditive gene expression in response to abiotic and biotic stresses.
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DOI：
10.1371/journal.pone.0024251
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Chen ZJ
中科院分区：
文献类型：
--
作者：
Kim ED;Chen ZJ
全基因组分析记录了植物和动物中密切相关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，15-43% 的基因在相关物种拟南芥和拟南芥之间表达不同，其中大多数在异源四倍体中非加性表达（与亲本中值不同）。非加性基因表达可由染色质修饰的转录调控引起，但转录后调控在非加性基因表达中的作用很大程度上未知。在这里，我们报告了重新合成的拟南芥异源四倍体中 mRNA 衰减的全基因组分析。在~26,000个注释基因中，超过1%的基因转录本表现出快速衰减，估计半衰期小于60分钟，它们被称为具有不稳定转录本的异源四倍体基因（AlloGUTs）。值得注意的是，30%的alloGUT与非加性表达的基因相匹配，并且它们的表达水平与衰减率呈负相关。与所有基因相比，这些非加性表达的 alloGUT 在基因本体论 (GOSlim) 分类中的比例高出 2-6 倍，以响应非生物和生物胁迫、信号转导和转录。有趣的是，AlloGUT 包括在应激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因子。这些数据表明 mRNA 稳定性在拟南芥异源多倍体同源基因表达中的作用。在拟南芥和其他异源多倍体（例如小麦和棉花）中，常见于胁迫相关途径中非加性表达基因的富集，这可能表明胁迫介导的生长活力在杂种和异源多倍体中发挥作用。
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.
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影响因子：
56.9
作者：
Harmer, SL;Hogenesch, LB;Kay, SA
通讯作者：
Kay, SA
影响因子：
4.4
作者：
Elkon R;Zlotorynski E;Zeller KI;Agami R
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影响因子：
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作者：
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影响因子：
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作者：
Covington, Michael F.;Maloof, Julin N.;Straume, Marty;Kay, Steve A.;Harmer, Stacey L.
通讯作者：
Harmer, Stacey L.
DOI：
10.1073/pnas.0807350106
发表时间：
2009-02-17
影响因子：
11.1
作者：
Ha, Misook;Kim, Eun-Deok;Chen, Z. Jeffrey
通讯作者：
Chen, Z. Jeffrey