Synthetic reversed sequences reveal default genomic states [Yeast_ATACseq]

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.解析基因组的默认状态，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，这使得我们无法明确观测到的基因组活性究竟是选择作用的结果，还是所谓的‘转录噪声’。为解答这一问题，我们将一段全新的101千碱基对（kb）基因座分别导入酿酒酵母（S. cerevisiae）与小家鼠（M. musculus）的基因组中，并对其基因组活性开展表征分析。该基因座的设计思路为：反向但不互补地引入人类次黄嘌呤磷酸核糖转移酶1（HPRT1）序列，包含大量侧翼区域，保留其基本序列特征，但消除其演化形成的编码与调控信息。我们观测到，在酿酒酵母中，反向与天然HPRT1基因座均呈现广泛的转录活性，尽管酿酒酵母本身并无适配该序列的演化型启动子。与之相反，该反向基因座在小鼠胚胎干细胞中完全无活性，反而呈现出抑制型染色质特征。缺失CpG二核苷酸（CpG dinucleotides）的基因座变体可缓解该抑制特征，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酿酒酵母中具有活性，但在小鼠胚胎干细胞中无活性，这与两种趋异真核细胞类型间存在的‘基因组默认状态’显著差异相符，该发现对理解广泛转录、遗传信息水平转移以及新基因诞生均具有重要参考价值。