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.

在动物中，RNA 聚合酶 II 从基因启动子开始双向转录，在正向链上产生前 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 PROMPT。在这里，我们对核 RNA 衰变缺陷的突变体（包括外泌体）进行稳态 RNA 测序，以重新评估拟南芥 PROMPT 的存在。虽然它们很罕见，但我们在拟南芥中发现了约 100 例外泌体敏感的 PROMPT。这种PROMPTs是外泌体缺陷突变体中小干扰RNA的来源，这或许可以解释为什么植物进化出了抑制PROMPTs的机制。此外，我们还发现了大约 200 个长的、未剪接的、外泌体敏感的反义 RNA，它们来自编码有义链上 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 GERMINATION1表达的非编码 RNA 是此类 RNA 的典型代表。转录因子基因在外泌体敏感的反义 RNA 基因座中过多，表明通过此类非编码 RNA 广泛控制基因表达的潜力。最后，我们评估了拟南芥中替代启动子的使用，并比较了现有 TSS 注释的准确性。