來自新加坡基因組研究院（Genome Institute of Singapore,，GIS）的研究人員近期報(bào)道了一種分析基因組三維折疊和環(huán)套狀態(tài)下，基因表達(dá)和調(diào)控的新技術(shù),。這一研究成果公布在Nature雜志上。
這種新技術(shù)即ChIA-PET (Chromatin Interaction Analysis using Paired End Tag sequencing),，其中PET是一種革新性的基因測(cè)序方法,，這種方法能幫助解決新一代測(cè)序平臺(tái)閱讀長(zhǎng)度較短的缺點(diǎn)問題，利用多種應(yīng)用的配對(duì)末端標(biāo)簽測(cè)序——PET測(cè)序,，從超高通量測(cè)序的常DNA片段末端引出短的配對(duì)標(biāo)簽,，從而就能精確地繪制基因組,。
領(lǐng)導(dǎo)這項(xiàng)研究的是GIS資深科學(xué)家阮義軍（Yijun Ruan），阮義軍博士曾領(lǐng)導(dǎo)新加坡基因組研究院研究小組獲得新加坡國(guó)家科學(xué)和技術(shù)獎(jiǎng),，這一獎(jiǎng)項(xiàng)是新加坡最高科學(xué)榮譽(yù),。其研究小組獲獎(jiǎng)原因是在配對(duì)端點(diǎn)雙標(biāo)記測(cè)序技術(shù)創(chuàng)新上取得開拓性研究成果，該技術(shù)可以用于全面展現(xiàn)人類基因組和轉(zhuǎn)錄特性,。
文章的第一作者是GIS阮義軍研究的Melissa Fullwood博士,，他說，“許多研究都表明遠(yuǎn)離基因的基因組區(qū)域在調(diào)控疾病方面的重要作用”,，“這到底是如何實(shí)現(xiàn)的呢,？一些科學(xué)家提出假設(shè)，認(rèn)為染色質(zhì)相互作用,，即DNA上的三維折疊幫助這些距離遠(yuǎn)的區(qū)域調(diào)控基因表達(dá),。”
自從科學(xué)家們發(fā)現(xiàn)人類基因組是通過三維立體的形式，而不是二維線性的形式進(jìn)行組織的,，他們就開始尋找分析這種三維結(jié)構(gòu)中基因活性調(diào)控的有效方法,。
在這篇文章中，GIS的研究人員利用ChIA-PET技術(shù)成功應(yīng)對(duì)了這一挑戰(zhàn),，證明了基因組中確實(shí)存在全基因組寬度的長(zhǎng)區(qū)域染色質(zhì)相互作用,。
人類基因組功能元件的深入理解，需要對(duì)個(gè)體基因組和染色體結(jié)構(gòu)的詳細(xì)巡查和比對(duì),，這就需要對(duì)DNA測(cè)序的通量和花費(fèi)進(jìn)行改進(jìn),。新一代測(cè)序平臺(tái)將是低花費(fèi)和高通量的，但其閱讀長(zhǎng)度較短,。這一限制的直接和普遍認(rèn)可的解決方法就是多種應(yīng)用的配對(duì)末端標(biāo)簽測(cè)序,，簡(jiǎn)稱為PET測(cè)序，從超高通量測(cè)序的常DNA片段末端引出短的配對(duì)標(biāo)簽,。PET測(cè)序能夠精確地繪制參考基因組,，區(qū)別PET所在DNA片段的基因組邊界和鑒定靶DNA片段。PET測(cè)序法已經(jīng)發(fā)展為轉(zhuǎn)錄組,，轉(zhuǎn)錄因子結(jié)合位點(diǎn)和染色體結(jié)構(gòu)分析,。PET測(cè)序技術(shù)的獨(dú)特優(yōu)點(diǎn)在于能夠暴露DNA片段兩末端的連接處。由于該優(yōu)點(diǎn),，PET測(cè)序可以解釋非傳統(tǒng)的融合轉(zhuǎn)錄物,，染色體結(jié)構(gòu)變化，甚至分子相互作用,。
利用這一方法,，研究人員發(fā)現(xiàn)了乳腺癌細(xì)胞中，人類基因組是如何應(yīng)答雌激素信號(hào),，進(jìn)行基因表達(dá)調(diào)控的,。GIS另外一位研究人員,，勞倫斯伯克力國(guó)家實(shí)驗(yàn)室基因組部主任Edward Rubin表示，“我們利用這種新方法回答了癌癥中的一些基礎(chǔ)問題,，結(jié)果發(fā)現(xiàn)基因組范圍內(nèi)的DNA高級(jí)相互作用能解釋一些之前研究中的矛盾情況,，這將有利于發(fā)展出對(duì)抗激素的治療乳腺癌新方法”。(生物谷Bioon.com)
生物谷推薦原始出處：
Nature 462, 58-64 (5 November 2009) | doi:10.1038/nature08497
An oestrogen-receptor--bound human chromatin interactome
Melissa J. Fullwood1, Mei Hui Liu1, You Fu Pan1, Jun Liu1, Han Xu1, Yusoff Bin Mohamed1, Yuriy L. Orlov1, Stoyan Velkov1, Andrea Ho1, Poh Huay Mei1, Elaine G. Y. Chew1, Phillips Yao Hui Huang1, Willem-Jan Welboren2, Yuyuan Han1, Hong Sain Ooi1, Pramila N. Ariyaratne1, Vinsensius B. Vega1, Yanquan Luo1, Peck Yean Tan1, Pei Ye Choy1, K. D. Senali Abayratna Wansa1, Bing Zhao1, Kar Sian Lim1, Shi Chi Leow1, Jit Sin Yow1, Roy Joseph1, Haixia Li1, Kartiki V. Desai1, Jane S. Thomsen1, Yew Kok Lee1, R. Krishna Murthy Karuturi1, Thoreau Herve1, Guillaume Bourque1, Hendrik G. Stunnenberg2, Xiaoan Ruan1, Valere Cacheux-Rataboul1, Wing-Kin Sung1,3, Edison T. Liu1, Chia-Lin Wei1, Edwin Cheung1,4,5 & Yijun Ruan1,4
1.Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
2.Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
3.Department of Computer Science, School of Computing, National University of Singapore, Singapore 117543
4.Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
5.School of Biological Sciences, Nanyang Technological University, Singapore 637551
Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor (ER-) in the human genome. We found that most high-confidence remote ER--binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER- functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.
