在過去的幾十年里我們讀取DNA的能力取得了巨大的進步,。但是對于我們來說，理解和改變遺傳代碼,，也就是說重新速寫DNA編碼的指令的能力還遠遠不足,。近日，來自魏茲曼研究所研究人員的一項研究推進了我們對于遺傳代碼的理解,，這種方法是將大量預(yù)先設(shè)計好的DNA片段引入活細胞的基因組中,，然后檢測其引入后對基因組的改變。這項研究刊登在了6月份的國際雜志Nature Biotechnology和Nature Genetics上,。
直到現(xiàn)在,，改變DNA序列一直是比較緩慢而且浪費人力物力的過程,。花費數(shù)周時間只能一次改變一個DNA控制區(qū),，隨后檢測其帶來的變化更是需要花費很多時間,。在這項研究中，研究者使用新技術(shù),，可以同時將成千上萬的DNA序列引入成千上萬個活細胞中（每一個DNA序列對應(yīng)一個活細胞）,。
“這種快速的技術(shù)可以幫助我們明顯加快理解DNA語言的能力”研究者Eran Segal表示，他還補充道,，讀出一個人的整個基因組序列是一件非常巨大的任務(wù),，畢竟基因組就還是一長串的字符串，而且有些部分難以理解,。破解DNA的字符串就好比是理解一種外國語言一樣,，我們的這樣技術(shù)可以幫助大家識別出DNA的詞語以及理解其意思。
理解DNA上書寫的信息可以幫助我們解釋,，不同人的基因型差異如何產(chǎn)生可觀察到的差異的,。比如，我們有可能去那種遺傳改變對個體疾病的發(fā)展負主要責(zé)任,，這項新技術(shù)也可以幫助我們在細胞中引入新的基因或者調(diào)節(jié)序列以修復(fù)機體的遺傳缺陷,。
這項研究中，科學(xué)家研究了DNA語言中重要的一方面,，那就是基因表達的控制如何受DNA的編碼影響,？也就是遺傳指令如何決定每個基因的活性？基因的活性水平對于正常細胞的功能必不可少,，這個問題是分子生物學(xué)長期以來的一個關(guān)鍵問題,。新技術(shù)可以幫助科學(xué)家分離并且檢測基因活性水平的效應(yīng)以及不同參數(shù)，比如一個基因的活性水平是如何受其調(diào)節(jié)序列和基因間的距離影響的,？研究者設(shè)法去闡明各種參數(shù)所表示的調(diào)節(jié)語言以及試圖去闡述遺傳序列的改變?nèi)绾斡绊懫涓淖兓蚧钚运降膮?shù),？
這種新方法結(jié)合了現(xiàn)有的技術(shù)，共包括四個步驟：1.在DNA芯片上創(chuàng)建50000個不同的遺傳序列,；2.將這些序列同時插入到細胞中,；3.在揀選機的幫助下將細胞分類以識別不同報道基因的表達；4.高通量DNA平行測序,。
這項研究由魏茲曼研究所,、以色列理工學(xué)院和安捷倫實驗室共同完成。（生物谷Bioon.com）
編譯自：Rewriting DNA to Understand What It Says
編譯者：T.Shen
doi:10.1038/nbt.2205
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PMID:
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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PMID:
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.
