Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa.
Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa.
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DOI：
10.1073/pnas.1807796115
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发表时间：
2018-11-27
影响因子：
11.1
通讯作者：
Birchler JA
中科院分区：
文献类型：
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作者：
Hou J;Shi X;Chen C;Islam MS;Johnson AF;Kanno T;Huettel B;Yen MR;Hsu FM;Ji T;Chen PY;Matzke M;Matzke AJM;Cheng J;Birchler JA
遗传平衡现象的特点是发现在整套染色体中增加或减少一条染色体比改变完整补体的剂量更有害。这一原理的分子基础以前还没有得到全面的研究。在这项研究中，研究了拟南芥中所有的5条三体染色体和二倍体、三倍体和四倍体的倍性序列，以研究基因表达调控。研究结果表明，基因组化学计量学对基因表达格局产生了影响，这对基因表达的运作方式、重复基因的进化以及数量性状的潜在基础都有影响。人们早就知道，部分基因组（非整倍性）剂量的变化比全基因组（倍性）数量的变化产生更严重的表型后果。为了研究这些差异的基础，我们研究了拟南芥所有五种三体以及二倍体、三倍体和四倍体成熟叶片组织中的基因表达。三体比倍体表现出更大的表达调节范围。总的来说，不同染色体上的基因表达从补偿到剂量效应不等，而基因组其余部分的基因表达从无影响到表达减少，接近染色体失衡的反向水平（2/3）。在每个基因型中检查全基因组DNA甲基化，发现在4三体中最明显的变化，但其他方面几乎没有变化，表明遗传失衡通常与DNA甲基化在机制上无关。对基因功能类别的独立分析表明，核糖体、蛋白酶体和基因体甲基化基因的调节程度低于所有类别的基因，而转录因子、信号转导成分和细胞器靶向蛋白基因则受到更紧密的反向影响。比较转录因子及其在三体和表达网络中的靶标揭示了相当大的不一致，说明调节化学计量的改变是遗传失衡的主要原因。对已发表的二体酵母和三体小鼠细胞基因表达数据的重新分析发现，在广泛的系统发育分类群中存在相似的化学计量效应，并表明这些效应反映了正常的基因调控过程。
The phenomenon of genetic balance is characterized by the finding that addition or subtraction of a single chromosome to the whole set is more detrimental than altering the dosage of the complete complement. The molecular basis of this principle has not been studied previously in a comprehensive manner. In this study, the set of all five trisomic chromosomes and a ploidy series of diploid, triploid, and tetraploid in Arabidopsis were examined for global gene expression modulations. The results indicate an impact of genomic stoichiometry on the landscape of gene expression, which has implications for how gene expression operates, the evolution of duplicate genes, and the underlying basis of quantitative traits. Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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影响因子：
4.6
作者：
Casanova-Sáez R;Candela H;Micol JL
通讯作者：
Micol JL
影响因子：
4.5
作者：
Emery M;Willis MMS;Hao Y;Barry K;Oakgrove K;Peng Y;Schmutz J;Lyons E;Pires JC;Edger PP;Conant GC
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Conant GC
影响因子：
56.9
作者：
Blakeslee, AF;Belling, J;Farnham, ME
通讯作者：
Farnham, ME
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3.8
作者：
Do C;Xing Z;Yu YE;Tycko B
通讯作者：
Tycko B
影响因子：
64.8
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