Synthetic reversed sequences reveal default genomic states

Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1,2,3,4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.多种物种中均存在广泛转录活性（pervasive transcriptional activity）。现存生物的基因组经历了数十亿年的演化，目前仍无法明确这些基因组活动究竟是选择作用的结果，还是所谓的转录噪声（transcriptional noise）。解析默认基因组状态（default genome states），有助于阐明广泛转录活性是否具有生物学意义。本研究通过将一段人工合成的101 kb基因座（locus）分别整合到酿酒酵母（Saccharomyces cerevisiae）和小家鼠（Mus musculus）的基因组中，并对基因组转录活性进行表征，以此解答该问题。该基因座的设计思路是将人类HPRT1（hypoxanthine phosphoribosyltransferase 1）基因及其侧翼序列进行反向反转，但不进行互补链替换，由此保留天然序列的基本特征，同时消除其演化而来的编码或调控信息。尽管酿酒酵母基因组中不存在该序列演化而来的启动子，但我们仍在酵母中观察到反向反转及天然HPRT1基因座均存在广泛的转录活性。与之形成对比的是，该反向反转基因座在小鼠胚胎干细胞（mouse embryonic stem cells）中完全无转录活性，反而呈现出阻抑性染色质特征（repressive chromatin signatures）。在缺失CpG二核苷酸（CpG dinucleotides）的基因座突变体中，这种阻抑性染色质特征得到了缓解；但即便如此，该突变体仍不具备转录活性。上述结果表明，缺乏编码信息的人工合成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，这与这两种演化分歧的真核细胞类型间存在的“默认基因组状态”差异相符，该发现对于理解广泛转录、遗传信息水平转移以及新基因诞生均具有参考价值。