Genome Res:翰霍普金斯大学Joel Bader与华大基因杨焕明联合发表酵母
12月11日，《genome Research》杂志上在线发表华大基因杨焕明教授与约翰霍普金斯大学Joel S. Bader研究员的一篇研究文章，文章指出研究人员证实SCRaMbLE能够在酵母人工染色体中有效生成指定组合的随机突变。杨焕明与Joel S. Bader为文章的通讯作者。
人工设计、合成和改造酵母染色体，是基因工程领域的热点研究方向。人们为此开发了许多实用工具，SCRaMbLE系统(Synthetic chromosome rearrangement and modification by loxP-mediated evolution)就是其中之一。该系统主要是通过重组酶位点的重排，获得不同组合的基因组多样性。研究人员将SCRaMbLE用于酵母人工染色体臂synIXR(43个重组酶位点)，并通过计算预测基因组的重组序列。随后他们对64个synIXR SCRaMbLE菌株进行深度测序，揭示了156个删除、89个倒置，95个重复和55个其他复杂重排。每个SCRaMbLE菌株都是独一无二的，说明SCRaMbLE有能力探索基因组的多样化空间。
研究显示，酵母基因组的重排只发生在人为设计的loxPsym位点。人工基因组区域、非人工基因组区域和线粒体基因组都没有明显的异常重排或者突变。研究指出，SCRaMbLE可以进一步扩大规模。同时介导多个合成染色体的进化。
原文链接：
SCRaMbLE GENErates designed combinatorial stochastic diversity in synthetic chromosomes
原文摘要：
Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 synIXR SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed loxPsym sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3′ UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.
作者：Joel Bader与杨焕明
