Synthetic reversed sequences reveal default genomic states [Yeast_CAGEseq]

Understanding default genome states would help interpret whether pervasive transcriptional activity has biological meaning. The genomes of extant organism have undergone billions of years of evolution, making it unclear whether observed genomic activities represent the effects of selection or “noise”. We addressed this question by introducing a novel 101-kb locus into the genomes of S. cerevisiae and M. musculus, and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including substantial flank-ing regions, retaining basic sequence features but ablating evolved coding or regulatory infor-mation. We observed widespread activity of both reversed and native HPRT1 loci in yeast, de-spite the lack of evolved yeast promoters. In contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, instead showing repressive chromatin signatures. The re-pressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless this variant too was transcriptionally inactive. These results show that novel genomic sequences lacking coding information are active in yeast, but inactive in mouse embryonic stem cells, con-sistent with a major difference in “default genomic states” between these two divergent eukary-otic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information, and new gene birth.解析默认基因组状态，有助于阐释广泛存在的转录活性是否具备生物学意义。现存生物的基因组历经数十亿年的演化，导致人们难以判断观测到的基因组活性究竟是选择作用的结果，还是所谓的“转录噪音”。本研究通过将一段全新的101千碱基位点分别整合至酿酒酵母（S. cerevisiae）与小家鼠（M. musculus）的基因组中，并对其基因组活性进行表征，以此解答这一问题。该位点的设计思路为，将人类HPRT1基因反向但不互补复制，同时引入其上下游的大量侧翼区域，保留基础序列特征，但消除其演化而来的编码与调控信息。尽管酿酒酵母自身并无该位点对应的演化型启动子，但我们观测到，反向与天然HPRT1位点在酵母中均呈现出广泛的转录活性。与之形成鲜明对比的是，该反向位点在小鼠胚胎干细胞中完全无转录活性，反而呈现出染色质抑制性特征。在缺失CpG二核苷酸的位点变体中，这种抑制性特征得到缓解，但该变体同样不具备转录活性。上述结果表明，缺乏编码信息的全新基因组序列在酵母中具有转录活性，但在小鼠胚胎干细胞中则无活性，这与这两类亲缘关系较远的真核细胞间存在的“默认基因组状态”显著差异相符，该发现对于阐释广泛转录现象、遗传信息水平转移以及新基因诞生等问题均具有重要参考价值。