Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways
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DOI：
10.1105/tpc.19.00815
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发表时间：
2020-03
期刊：
影响因子：
11.6
通讯作者：
Axel Thieffry;M. Vigh;Jette Bornholdt;M. Ivanov;P. Brodersen;A. Sandelin
中科院分区：
文献类型：
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作者：
Axel Thieffry;M. Vigh;Jette Bornholdt;M. Ivanov;P. Brodersen;A. Sandelin
我们报告存在的双向转录位点产生外泌体敏感的RNA在拟南芥中，其中产生的RNA是小干扰RNA的来源，和外泌体敏感的转录本反义基因编码的调控蛋白，特别是转录因子。在动物中，RNA聚合酶II从基因启动子双向启动转录，在正链上产生前mRNA，在反向链上产生启动子上游转录物（PROMPT）。PROMPT被核外泌体降解。先前基于新生RNA方法的研究得出结论，拟南芥（Arabidopsis thaliana）不产生PROMPTs。在这里，我们使用稳态RNA测序突变体核RNA衰变缺陷，包括外泌体重新评估拟南芥PROMPTs的存在。虽然它们很罕见，但我们在拟南芥中鉴定了100例外泌体敏感的PROMPTs。这种PROMPTs是外来体缺陷突变体中小干扰RNA的来源，这也许可以解释为什么植物已经进化出抑制PROMPTs的机制。此外，我们还发现了约200个长的、未剪接的、对外来体敏感的反义RNA，这些反义RNA来自编码正义链上3′-非翻译区的基因组部分内的转录起始位点。先前表征的调节关键种子休眠调节因子DELAY OF GERMINATION 1表达的非编码RNA是这类RNA的典型代表。转录因子基因在具有外泌体敏感性反义RNA的基因座中的比例过高，这表明通过这类非编码RNA广泛控制基因表达的潜力。最后，我们评估了替代启动子在拟南芥中的使用，并比较现有TSS注释的准确性。
We report the existence of bidirectionally transcribed loci producing exosome-sensitive RNAs in Arabidopsis in which the produced RNAs are sources of small interfering RNAs, and exosome-sensitive transcripts antisense to genes encoding regulatory proteins, in particular transcription factors. In animals, RNA polymerase II initiates transcription bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis (Arabidopsis thaliana) does not produce PROMPTs. Here, we used steady-state RNA sequencing in mutants defective in nuclear RNA decay including the exosome to reassess the existence of Arabidopsis PROMPTs. While they are rare, we identified ∼100 cases of exosome-sensitive PROMPTs in Arabidopsis. Such PROMPTs are sources of small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPTs. In addition, we found ∼200 long, unspliced and exosome-sensitive antisense RNAs that arise from transcription start sites within parts of the genome encoding 3′-untranslated regions on the sense strand. The previously characterized noncoding RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of noncoding RNAs. Lastly, we assess the use of alternative promoters in Arabidopsis and compare the accuracy of existing TSS annotations.