在过去的几十年里我们读取DNA的能力取得了巨大的进步。但是对于我们来说，理解和改变遗传代码，也就是说重新速写DNA编码的指令的能力还远远不足。近日，来自魏兹曼研究所研究人员的一项研究推进了我们对于遗传代码的理解，这种方法是将大量预先设计好的DNA片段引入活细胞的基因组中，然后检测其引入后对基因组的改变。这项研究刊登在了6月份的国际杂志Nature Biotechnology和Nature Genetics上。
直到现在，改变DNA序列一直是比较缓慢而且浪费人力物力的过程。花费数周时间只能一次改变一个DNA控制区，随后检测其带来的变化更是需要花费很多时间。在这项研究中，研究者使用新技术，可以同时将成千上万的DNA序列引入成千上万个活细胞中（每一个DNA序列对应一个活细胞）。
“这种快速的技术可以帮助我们明显加快理解DNA语言的能力”研究者Eran Segal表示，他还补充道，读出一个人的整个基因组序列是一件非常巨大的任务，毕竟基因组就还是一长串的字符串，而且有些部分难以理解。破解DNA的字符串就好比是理解一种外国语言一样，我们的这样技术可以帮助大家识别出DNA的词语以及理解其意思。
理解DNA上书写的信息可以帮助我们解释，不同人的基因型差异如何产生可观察到的差异的。比如，我们有可能去那种遗传改变对个体疾病的发展负主要责任，这项新技术也可以帮助我们在细胞中引入新的基因或者调节序列以修复机体的遗传缺陷。
这项研究中，科学家研究了DNA语言中重要的一方面，那就是基因表达的控制如何受DNA的编码影响？也就是遗传指令如何决定每个基因的活性？基因的活性水平对于正常细胞的功能必不可少，这个问题是分子生物学长期以来的一个关键问题。新技术可以帮助科学家分离并且检测基因活性水平的效应以及不同参数，比如一个基因的活性水平是如何受其调节序列和基因间的距离影响的？研究者设法去阐明各种参数所表示的调节语言以及试图去阐述遗传序列的改变如何影响其改变基因活性水平的参数？
这种新方法结合了现有的技术，共包括四个步骤：1.在DNA芯片上创建50000个不同的遗传序列；2.将这些序列同时插入到细胞中；3.在拣选机的帮助下将细胞分类以识别不同报道基因的表达；4.高通量DNA平行测序。
这项研究由魏兹曼研究所、以色列理工学院和安捷伦实验室共同完成。（生物谷Bioon.com）
编译自：Rewriting DNA to Understand What It Says
编译者：T.Shen
doi:10.1038/nbt.2205
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Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
Eilon Sharon,1, 2, 5 Yael Kalma,1, 2, 5 Ayala Sharp,2 Tali Raveh-Sadka,1 Michal Levo,1 Danny Zeevi,1, 2 Leeat Keren,1, 2 Zohar Yakhini,3, 4 Adina Weinberger1, 2 & Eran Segal1,
Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited. We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.
doi:10.1038/ng.2305
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Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
Tali Raveh-Sadka,1, 2, 4 Michal Levo,1, 2, 4 Uri Shabi,3 Boaz Shany,1, 2 Leeat Keren,1, 2 Maya Lotan-Pompan,1, 2 Danny Zeevi,1, 2 Eilon Sharon,1, 2 Adina Weinberger1, 2 & Eran Segal1, 2
Understanding how precise control of gene expression is specified within regulatory DNA sequences is a key challenge with far-reaching implications. Many studies have focused on the regulatory role of transcription factor–binding sites. Here, we explore the transcriptional effects of different elements, nucleosome-disfavoring sequences and, specifically, poly(dA:dT) tracts that are highly prevalent in eukaryotic promoters. By measuring promoter activity for a large-scale promoter library, designed with systematic manipulations to the properties and spatial arrangement of poly(dA:dT) tracts, we show that these tracts significantly and causally affect transcription. We show that manipulating these elements offers a general genetic mechanism, applicable to promoters regulated by different transcription factors, for tuning expression in a predictable manner, with resolution that can be even finer than that attained by altering transcription factor sites. Overall, our results advance the understanding of the regulatory code and suggest a potential mechanism by which promoters yielding prespecified expression patterns can be designed.
