The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes
The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes
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DOI：
10.1371/journal.pgen.1008268
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发表时间：
2019-07-01
期刊：
影响因子：
4.5
通讯作者：
Hudson, Quanah J.
中科院分区：
文献类型：
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作者：
Andergassen, Daniel;Muckenhuber, Markus;Hudson, Quanah J.
长链非编码（lnc）RNA在哺乳动物基因组中有很多，并且许多被认为参与基因表达的调控。然而，大多数仍然相对未被描述和不确定的功能，使使用模型系统来揭示其作用模式的价值。印迹lncRNA靶向并募集表观遗传沉默因子到同一染色体上的印迹基因簇，使其成为顺式沉默远缘基因的最佳表征lncRNA之一。在这项研究中，我们研究了在小鼠Igf 2 r印迹簇中的lncRNA Airn对远距离印迹基因Slc 22 a3的沉默。以前我们提出印迹lncRNA可能通过增强子转录破坏启动子-增强子相互作用来沉默遥远的印迹基因，我们称之为增强子干扰假说。在这里，我们通过首先使用等位基因特异性染色体构象捕获（3C）来检测Slc 22 a3启动子和使其在父本染色体上沉默的Airn lncRNA的基因座之间的相互作用来测试该假设。与该模型一致，我们发现在整个Airn基因上的母体等位基因上富集的相互作用与多个增强子-启动子相互作用一致。因此，为了测试增强子干扰假说，我们设计了一种删除整个Airn基因的方法。然而，该缺失表明Airn基因内没有Slc 22 a2、Pde 10a和Slc 22 a3的必需增强子，这强烈表明Airn RNA而不是其转录负责沉默远距离印迹基因。此外，我们发现沉默的印记基因被抑制的父系等位基因上的大块H3 K27 me 3覆盖。因此，我们提出了另一种假设，即染色体相互作用可能最初引导lncRNA靶向印迹启动子并招募抑制性染色质，并且一旦沉默建立，这些相互作用就会丢失。
Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.