Synthetic reversed sequences reveal default genomic states [Yeast_ChIPseq]

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演化，导致人们难以判断观测到的基因组活性究竟是自然选择的作用结果，还是所谓的“转录噪音”。本研究通过向酿酒酵母（Saccharomyces cerevisiae, S. cerevisiae）和小家鼠（Mus musculus, M. musculus）的基因组中引入一段全新的101 kb基因座（locus），并对基因组活性进行表征，以此解答上述问题。该基因座的构建方式为：将人类次黄嘌呤磷酸核糖转移酶1（hypoxanthine phosphoribosyltransferase 1, HPRT1）序列反向但不互补，同时纳入大量侧翼区域，保留其基本序列特征，但去除演化而来的编码或调控信息。我们观测到，尽管酿酒酵母本身不存在适配该序列的演化启动子，但反向及天然HPRT1基因座在酵母中均呈现广泛的转录活性。与之形成对比的是，该反向基因座在小鼠胚胎干细胞中完全无活性，反而呈现出阻遏型染色质特征。缺失CpG二核苷酸（CpG dinucleotides）的基因座变体可缓解这种阻遏特征，但该变体同样无法产生转录活性。上述结果表明，缺乏编码信息的全新基因组序列在酿酒酵母中具有转录活性，但在小鼠胚胎干细胞中则无活性，这与这两种趋异真核细胞类型间存在的“默认基因组状态”显著差异相一致，该发现对阐释广泛转录、遗传物质水平转移以及新基因诞生等问题具有参考价值。