Genetic compensation is triggered by mutant mRNA degradation

Genetic compensation by transcriptional modulation of related gene(s) (also known as transcriptional adaptation) has been reported in numerous systems1-3; however, whether and how such a response can be activated in the absence of protein feedback loops is unknown. Here, we develop and analyze several models of transcriptional adaptation in zebrafish and mouse that we show are not caused by loss of protein function. We find that the increase in transcript levels is due to enhanced transcription, and observe a correlation between the levels of mutant mRNA decay and transcriptional upregulation of related genes. To assess the role of mutant mRNA degradation in triggering transcriptional adaptation, we use genetic and pharmacological approaches and find that mRNA degradation is indeed required for this process. Notably, uncapped RNAs, themselves subjected to rapid degradation, can also induce transcriptional adaptation. Next, we generate alleles that fail to transcribe the mutated gene and find that they do not show transcriptional adaptation, and exhibit more severe phenotypes than those observed in alleles displaying mutant mRNA decay. Transcriptome analysis of these different alleles reveals the upregulation of hundreds of genes with enrichment for those showing sequence similarity with the mutated gene's mRNA, suggesting a model whereby mRNA degradation products induce the response via sequence similarity. These results expand the role of the mRNA surveillance machinery in buffering against mutations by triggering the transcriptional upregulation of related genes. Besides implications for our understanding of disease-causing mutations, our findings will help design mutant alleles with minimal transcriptional adaptation-derived compensation. Examination of transcriptional adaptation based on 3 genes in 3 cell types. Actb was assessed in ESCs as a K.O. and full locus deletion and compared versus wild type (2 replicates each). Actg1 was assessed in MEFs as a K.O. and full locus deletion and compared versus wild type (2 replicates each). Kindlin 2 was assessed in MKFs as a K.O. and and compared versus floxed (2 replicates each).转录适应（transcriptional adaptation），即通过对相关基因进行转录调控实现的遗传补偿，已在诸多研究体系中被报道1-3；然而，在不存在蛋白质反馈环路的情况下，该响应是否可以被激活、以及其具体激活机制如何，目前仍尚不明确。本研究构建并分析了斑马鱼与小鼠中的数种转录适应模型，证实这些模型并非由蛋白质功能丧失所导致。我们发现转录本水平的升高源于转录过程的增强，同时观察到突变mRNA的降解水平与相关基因的转录上调程度之间存在显著相关性。为了评估突变mRNA降解在触发转录适应中的作用，我们采用遗传学与药理学手段开展研究，结果证实mRNA降解确实是该过程不可或缺的一环。值得注意的是，自身会被快速降解的未加帽RNA，同样能够诱导转录适应。随后，我们构建了无法转录突变基因的等位基因，结果发现这些等位基因不会表现出转录适应，且其表型比出现突变mRNA降解的等位基因更为严重。对这些不同等位基因的转录组分析显示，数百个基因出现上调，其中显著富集与突变基因mRNA序列相似的基因，这提示了一种模型：mRNA降解产物通过序列相似性诱导该响应。这些结果拓展了mRNA监视系统的功能范畴，其可通过触发相关基因的转录上调来缓冲突变带来的负面影响。除了对我们理解致病突变具有重要启示之外，本研究结果还有助于设计出受转录适应介导的补偿效应最弱的突变等位基因。本研究基于3种细胞类型中的3个基因开展转录适应检测：以胚胎干细胞（ESCs）为模型，对Actb基因的敲除（K.O.）与全基因座缺失样本进行检测，并与野生型样本进行对照，每组设置2个生物学重复；以小鼠胚胎成纤维细胞（MEFs）为模型，对Actg1基因的敲除与全基因座缺失样本进行检测，并与野生型样本进行对照，每组设置2个生物学重复；以巨核细胞成纤维细胞（MKFs）为模型，对Kindlin 2基因的敲除（K.O.）样本进行检测，并与floxed等位基因样本进行对照，每组设置2个生物学重复。