In animals, transcription by RNA polymerase II initiates 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 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 A. thaliana PROMPTs. While PROMPTs are overall rare in A. thaliana, ~100 cases of exosome-sensitive PROMPTs were identified. 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 transcription start sites within 3'-UTR-encoding regions that produce long unspliced, exosome-sensitive antisense RNAs. The previously characterized non-coding (nc) 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 ncRNAs. Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

在动物中，RNA聚合酶II的转录从基因启动子双向启动，从而在正向链上产生前mRNA，在反向链上产生启动子上游转录本（PROMPT）。PROMPT被核外泌体降解。以前基于新生RNA方法的研究得出结论，拟南芥不产生PROMPT。在这里，我们对包括外泌体在内的核RNA衰变有缺陷的突变体使用稳态RNA测序，以重新评估拟南芥PROMPT的存在。虽然PROMPT在拟南芥中总体上很少见，但已鉴定出约100例对外泌体敏感的PROMPT。此类PROMPT是外泌体缺陷型突变体中小干扰RNA的来源，也许可以解释为什么植物已经进化出抑制PROMPT的机制。此外，我们在3'内发现了约200个转录起始位点 -UTR编码区，可产生长的未剪接，外来体敏感的反义RNA。以前表征非编码（nc）的RNA调节关键种子休眠调节剂DELAY OF GERMINATION1的表达，是此类RNA的典型代表。转录因子基因在外来体敏感的反义RNA中位点过高，这表明通过此类ncRNA广泛控制基因表达的潜力。最后，我们评估拟南芥中替代启动子的使用，并比较现有TSS注释的准确性。转录因子基因在外来体敏感的反义RNA中位点过高，这表明通过此类ncRNA广泛控制基因表达的潜力。最后，我们评估拟南芥中替代启动子的使用，并比较现有TSS注释的准确性。转录因子基因在外来体敏感的反义RNA中位点过高，这表明通过此类ncRNA广泛控制基因表达的潜力。最后，我们评估拟南芥中替代启动子的使用，并比较现有TSS注释的准确性。