Eukaryotic promoter regions are frequently divergently transcribed in vivo, but it is unknown whether the resultant antisense RNAs are a mechanistic by-product of RNA polymerase II (Pol II) transcription or biologically meaningful. Here, we use a functional evolutionary approach that involves nascent transcript mapping in S. cerevisiae strains containing foreign yeast DNA. Promoter regions in foreign environments lose the directionality they have in their native species. Strikingly, fortuitous promoter regions arising in foreign DNA produce equal transcription in both directions, indicating that divergent transcription is a mechanistic feature that does not imply a function for these transcripts. Fortuitous promoter regions arising during evolution promote bidirectional transcription and over time are purged through mutation or retained to enable new functionality. Similarly, human transcription is more bidirectional at newly evolved enhancers and promoter regions. Thus, promoter regions are intrinsically bidirectional and are shaped by evolution to bias transcription toward coding versus non-coding RNAs.

中文翻译：

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启动子区域定向性的基态和演化。

真核启动子区域经常在体内转录，但未知的反义RNA是RNA聚合酶II（Pol II）转录的机制副产物还是生物学意义的。在这里，我们使用一种功能进化的方法，该方法涉及在含有外源酵母DNA的酿酒酵母菌株中进行新生的转录本作图。外国环境中的促进者地区失去了其本土物种所具有的方向性。令人惊讶地，在外源DNA中产生的偶然启动子区域在两个方向上产生相等的转录，表明发散转录是机制特征，并不暗示这些转录物具有功能。在进化过程中产生的偶然启动子区域促进双向转录，并随着时间的流逝通过突变清除或保留以实现新功能。同样，人类转录在新形成的增强子和启动子区域更双向。因此，启动子区域本质上是双向的，并且通过进化而成形，以使转录偏向于编码与非编码RNA。