来自新加坡基因组研究院(Genome Institute of Singapore,GIS)的研究人员近期报道了一种分析基因组三维折叠和环套状态下,基因表达和调控的新技术。这一研究成果公布在Nature杂志上。
这种新技术即ChIA-PET (Chromatin Interaction Analysis using Paired End Tag sequencing),其中PET是一种革新性的基因测序方法,这种方法能帮助解决新一代测序平台阅读长度较短的缺点问题,利用多种应用的配对末端标签测序——PET测序,从超高通量测序的常DNA片段末端引出短的配对标签,从而就能精确地绘制基因组。
领导这项研究的是GIS资深科学家阮义军(Yijun Ruan),阮义军博士曾领导新加坡基因组研究院研究小组获得新加坡国家科学和技术奖,这一奖项是新加坡最高科学荣誉。其研究小组获奖原因是在配对端点双标记测序技术创新上取得开拓性研究成果,该技术可以用于全面展现人类基因组和转录特性。
文章的第一作者是GIS阮义军研究的Melissa Fullwood博士,他说,“许多研究都表明远离基因的基因组区域在调控疾病方面的重要作用”,“这到底是如何实现的呢?一些科学家提出假设,认为染色质相互作用,即DNA上的三维折叠帮助这些距离远的区域调控基因表达。”
自从科学家们发现人类基因组是通过三维立体的形式,而不是二维线性的形式进行组织的,他们就开始寻找分析这种三维结构中基因活性调控的有效方法。
在这篇文章中,GIS的研究人员利用ChIA-PET技术成功应对了这一挑战,证明了基因组中确实存在全基因组宽度的长区域染色质相互作用。
人类基因组功能元件的深入理解,需要对个体基因组和染色体结构的详细巡查和比对,这就需要对DNA测序的通量和花费进行改进。新一代测序平台将是低花费和高通量的,但其阅读长度较短。这一限制的直接和普遍认可的解决方法就是多种应用的配对末端标签测序,简称为PET测序,从超高通量测序的常DNA片段末端引出短的配对标签。PET测序能够精确地绘制参考基因组,区别PET所在DNA片段的基因组边界和鉴定靶DNA片段。PET测序法已经发展为转录组,转录因子结合位点和染色体结构分析。PET测序技术的独特优点在于能够暴露DNA片段两末端的连接处。由于该优点,PET测序可以解释非传统的融合转录物,染色体结构变化,甚至分子相互作用。
利用这一方法,研究人员发现了乳腺癌细胞中,人类基因组是如何应答雌激素信号,进行基因表达调控的。GIS另外一位研究人员,劳伦斯伯克力国家实验室基因组部主任Edward Rubin表示,“我们利用这种新方法回答了癌症中的一些基础问题,结果发现基因组范围内的DNA高级相互作用能解释一些之前研究中的矛盾情况,这将有利于发展出对抗激素的治疗乳腺癌新方法”。(生物谷Bioon.com)
生物谷推荐原始出处:
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.