欲穷千里目,更上一层楼戴俊彪 欲实时把握基因组xx / 合成生物学理论，技术和应用的最新进展，请参与第一届基因组xx /合成生物学的理论和应用研究研讨会（2021年 6月 8 -10日，上海）。点击文末“阅读原文”，即可注册第一届基因组xx /合成生物学的理论和应用研究研讨会（2021年 6月 8 -10日，上海）。戴俊彪专题汇报Decode and reprogram the yeast genome(6月 10日 17:30-18:00pm)New technologies to synthesize DNA, facilitated by methods exploiting synthesis of oligonucleotides on microarrays for example, provides a great opportunity to completely redesign the entire genome of an organism. Together with several other groups worldwide, we aim to re-synthesize a designer eukaryotic genome, In my lab, a 976,067-base pair linear chromosome, synXII, was designed and assembled using a two-step method, producing a functional chromosome. The ribosomal gene cluster (rDNA) on synXII is retained during the assembly process and subsequently replaced by a modified rDNA unit used to regenerate rDNA at three distinct chromosomal locations. The signature sequences within rDNA, commonly used as the molecule barcode of a species, are swapped to generate a Saccharomyces strain that would be identified as Saccharomyces bayanus. Furthermore, as a novel inducible system implemented in the synthetic chromosomes, SCRaMbLE is designed to generate diverse genotypes and phenotypes by massive chromosome rearrangements. We have designed a reporter of SCRaMbLEd cells using efficient selection, termed ReSCuES, based on a loxP-mediated switch of two auxotrophic markers. We show that all randomly isolated clones contained rearrangements within the synthetic chromosome, demonstrating high efficiency of selection. Using ReSCuES, we illustrate, for the first time, the ability of SCRaMbLE to generate strains with increased tolerance to several stress factors, such as ethanol, heat and acetic acid. In addition, by analyzing the tolerant strains, we are able to identify ACE2, a transcription factor required for septum destruction after cytokinesis, as a negative regulator of ethanol tolerance. Collectively, our work not only offers a new avenue of decoding the yeast genome through intelligent design followed by chemical synthesis, but also demonstrates our ability to reprogram the genome for future applications.科研结果戴俊彪教授基因xx相关及代表性文章：Huang#, Zhouqing Luo#, Wantao Ying#, Qichen Cao, He Huang, Junkai Dong, Qingyu Wu, Yingming Zhao, Xiaohong Qian*, Junbiao Dai*, 2-hydroxyisobutyrylation on histone H4K8 is regulated by glucose homeostasis in Saccharomyces cerevisiae, PNAS, 2021, 114(33):8782-8787. doi: / (*: Co-corresponding authors)利用质谱技术和遗传生化手段，研究者对酵母中 H4K8的 2 -羟基异丁酰基化（H4K8hib）水平调控机理进行了具体的论述。首先，经过筛选发觉在酵母中碳源饥饿的条件下能够造成 H4K8hib的水平显著下降，在培养基中补充葡萄糖或果糖能够快速恢复其修饰水平。其次，H4K8hib的水平的下降是由两个组蛋白去乙酰化酶 Rpd3p和 Hos3p介导的，且其去乙酰化活性位点对于去 2 -羟基异丁酰活性是必须的。第三，当 H4K8突变成 H4K8A后，酵母的时序寿命显著缩短，说明 H4K8位点的酰化修饰在酵母衰老过程中存在着主要的功效。最终，经过蛋白质组学的研究发觉 2 -羟基异丁酰基化修饰和葡萄糖代谢之间含有紧密联络。该研究结果发表在美国科学院院刊（PNAS）上，首次在体内判定到了 2 -羟基异丁酰修饰的去修饰酶，并建立了该修饰和细胞时序寿命和葡萄糖代谢之间的网络关系。Zhang#, Guanghou Zhao#, Zhouqing Luo#, Yicong Lin, Lihui Wang, Yakun Guo, Ann Wang, Shuangying Jiang, Qingwen Jiang, Jianhui Gong, Yun Wang, Sha Hou, Jing Huang, Tianyi Li, Yiran Qin, Junkai Dong, Qin Qin, Jiaying Zhang, Xinzhi Zou, Xi He, Li Zhao, Yibo Xiao, Meng Xu, Erchao Cheng, Ning Huang, Tong Zhou, Yue Shen, Roy Walker, Yisha Luo, Zheng Kuang, Leslie A. Mitchell, Kun Yang, Sarah M. Richardson, Yi Wu, Bing-Zhi Li, Ying-Jin Yuan, Huanming Yang, Jiwei Lin, Guo-Qiang Chen, Qingyu Wu, Joel S. Bader, Yizhi Cai, Jef D. Boeke, Junbiao Dai*, Engineering the ribosomal DNA in a megabase synthetic chromosome, Science, 355(6329), pii: eaaf3981. doi: /能否在试验室结构含有生命特征的细胞一直是一个主要挑战，也是对生命起源的不懈探索。研究人员以真核生物酿酒酵母第 XII号染色体为研究对象，利用合成生物学工程化设计的理念对酵母基因组进行重新设计和改造，包含消除基因组中的转座子、反复序列等可能的冗余元件，同时加入特定元件（loxPsym序列），经过化学合成手段最终取得了一条含有良好生物学功效的长度为 976,067个碱基正确人工酵母 XII号染色体。另外，经过对酵母核仁的主要组成成份 rDNA区域的删除、重建和 ITS序列的置换，证实了酵母中 rDNA区域含有惊人的灵活度和可塑性。经过以上对酵母基因组的人工设计和合成，研究者能够更透彻的了解遗传物质发挥功效的生物学机制、遗传信息的传输和调控，从而帮助人类有目标地设计和改造生命体，实现预设功效，以期处理人类在发展过程中面临的环境和能源方面的重大挑战。该研究结果以封面形式发表在 Science杂志上，一经发表便在国际上得到了 Nature News、Science News等科学杂志和华盛顿邮报、路透社等媒体的广泛报道。我国人民日报社、新华通报社和科技日报等众多媒体全部做了长篇报道，科技部就该研究结果公布科技动态标志“中国真核人工基因组合成研究水平进入国际前列”。Mercy, Julien Mozziconacci, Vittore F. Scolari, Kun Yang, Guanghou Zhao, Thierry, Yisha Luo, Leslie A. Mitchell, Michael Shen, Yue Shen, Roy Walker, Weimin Zhang, Yi Wu, Ze-xiong Xie, Zhouqing Luo, Yizhi Cai, Junbiao Dai, Huanming Yang, Ying-Jin Yuan, Jef D. Boeke, Joel S. Bader, Heloise Muller*, Romain Koszul*, 3D organization of synthetic and scrambled chromosomes, Science, 355(6329), pii: eaaf4597. doi: / (*: Co-corresponding authors)利用 Hi- C染色体构象捕捉技术，研究人员解析了酵母染色体的三维空间结构。然而针对 项目标人工合成染色体而言，tRNA的移除、逆转座子的删除和 rDNA区域的异位重建等改变是否会打破酵母染色体稳定的空间结构？经过大量的研究证实，合成染色体序列的改变对整合基因组的高级结构不产生显著影响，然而，rDNA区域在其它染色体上重建能够造成 XII号染色体和核仁在细胞内的位置改变，同时造成染色体高级结构的调整。除此之外，合成型酵母染色体因为删除了大量的反复序列元件，目标是增加人工染色体的稳定性，最终使得染色体之间的互作图谱相对野生型愈加清楚。该研究结果和 synXII的合成和功效研究工作同时以封面形式发表在 Science杂志上，在国际上得到了众多科学杂志和媒体的广泛报道。想和戴俊彪教授“面对面”探讨交流吗？点击“阅读原文”，即可报名参与“第一届基因组xx /生物合成学的基础和应用研究研讨会”。