RNA sequence (RNA-seq) profiling of SynIX strain

We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. We found that both synIX transfer via chromoduction and wild-type IX destabilization were efficient methods. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these two chromosomes.本研究完整报道了一条长度为404963碱基对（base pair, bp）的人工合成酵母九号染色体synIX的合成、组装、调试与表征全过程。我们采用组合式染色体构建方法，完成了synIX左臂（synIXL）的合成，并对此前已报道的synIXR进行了改造升级。在synIX菌株表征过程中，我们发现并修复了一处与EST3基因相关的缺陷——该基因参与端粒酶功能调控，最终获得了适合度接近野生型菌株的synIX工程菌株。为便于后续人工合成染色体的整合，并提升不同菌株间染色体转移的灵活性，我们将染色体转导（chromoduction）——一种可在两株菌株间转移整条染色体的技术——与条件性着丝粒去稳定化技术相结合，实现了目标染色体对其天然同源染色体的替换。实验结果表明，通过染色体转导进行synIX转移，以及对野生型九号染色体进行去稳定化处理，均为高效的染色体替换方法。我们观察到，野生型二号染色体倾向于与synIX共转移，并可与野生型九号染色体共同发生去稳定化，这暗示这两条染色体之间存在潜在的基因剂量补偿效应。