最新Nature：基因组新技术

　　

生物通报道：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”。

（生物通：张迪）

附：

EDUCATION

1995-1996 Post-doctoral Fellow, Program of Gene Discovery and Gene Expression, Monsanto Company, St Louis, Missouri, USA
1990-1994 Doctor of philosophy in Plant Molecular Biology, University of Maryland, College Park, Maryland, USA


PROFESSIONAL APPOINTMENTS

2003 Associate Director, Genome Technology Genome Institute of Singapore
2002 Senior Group Leader, Genome Technology and Biology Genome Institute of Singapore
1999-2002 Director, Core Genomics and Applications Large Scale Biology Corporation, Vacaville, California, USA
1996-1999 Senior Scientist, Genome Technology, Monsanto Company, St. Louis, Missouri, USA

HONORS AND AWARDS

2006 National Science Award 2006, Singapore
1998-2001 Rockefeller Foundation Fellow Helped China to initiate rice functional genomics research sponsored by Rockefeller Foundation under a rice biotech fellowship program.
1995 Carroll E. Cox Graduate Research Excellence Award, University of Maryland, 1995. For the best Ph.D dissertation in biology submitted in 1994

EXTERNAL GRANT

9/2007-8/2010 Paired-end ditag technology for complete annotation of fusion genes by NIH/NCI, Cancer genome technology development (US$ 1,215,150)
9/2007-10/2011 Comprehensive Characterization and Classification of the Human Transcriptome by NIH/NHGRI (U54 HG004557), an ENCODE scale up grant (US$1,101,702)
9/2007-10/2010 Whole Genome Chromatin Interaction Analysis using Pair-End-diTagging (ChIA-PET) by NIH/NHGRI (1 R01 HG004456-01), an ENCODE technology development grant (US$990,000)
9/2004-10/2007 Ditag Technologies for Complete Transcriptome Annotation by NIH/NHGRI (1R01HG003521-01), an ENCODE technology development grant (US$1,001,452)
11/2006-5/2008 Viral Metagenome by DARPA, DOD USA (US$360,000)
11/2003-5/2004 Zebrafish Gene Collection: Selection of Full-length cDNA Clones Using Colony Array Hybridization and EST sequencing by NIH/NIDDK, an MGC contract grant (US$613,036)
1/2007-12/2007 Large insert size PET technology development by ROCHE DIAGNOSTICS GMBH (US$75,000)


SELECTED PUBLICATIONS

1. Fullwood Melissa J, Wei Chia-Lin, Liu Edison T, Ruan Yijun "Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses." Genome Res. 2009 Apr ; 19(4) : 521-32
Abstract
2. Desnues Christelle, Rodriguez-Brito Beltran, Rayhawk Steve, Kelley Scott, Tran Tuong, Haynes Matthew, Liu Hong, Furlan Mike, Wegley Linda, Chau Betty, Ruan Yijun, Hall Dana, Angly Florent E, Edwards Robert A, Li Linlin, Thurber Rebecca Vega, Reid R Pamela, Siefert Janet, Souza Valeria, Valentine David L, Swan Brandon K, Breitbart Mya, Rohwer Forest "Biodiversity and biogeography of phages in modern stromatolites and thrombolites." Nature 2008 Mar 20 ; 452(7185) : 340-3 Epub 2008 Mar 2
Abstract
3. Chen Xi, Xu Han, Yuan Ping, Fang Fang, Huss Mikael, Vega Vinsensius B, Wong Eleanor, Orlov Yuriy L, Zhang Weiwei, Jiang Jianming, Loh Yuin-Han, Yeo Hock Chuan, Yeo Zhen Xuan, Narang Vipin, Govindarajan Kunde Ramamoorthy, Leong Bernard, Shahab Atif, Ruan Yijun, Bourque Guillaume, Sung Wing-Kin, Clarke Neil D, Wei Chia-Lin, Ng Huck-Hui "Integration of external signaling pathways with the core transcriptional network in embryonic stem cells." Cell 2008 Jun 13 ; 133(6) : 1106-17
Abstract
4. ENCODE (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (7146):799-816.

5. Ruan Yijun, Ooi Hong Sain, Choo Siew Woh, Chiu Kuo Ping, Zhao Xiao Dong, Srinivasan K G, Yao Fei, Choo Chiou Yu, Liu Jun, Ariyaratne Pramila, Bin Wilson G W, Kuznetsov Vladimir A, Shahab Atif, Sung Wing-Kin, Bourque Guillaume, Palanisamy Nallasivam, Wei Chia-Lin "Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)." Genome Res. 2007 Jun ; 17(6) : 828-38
Abstract
6. Wei Chia-Lin, Wu Qiang, Vega Vinsensius B, Chiu Kuo Ping, Ng Patrick, Zhang Tao, Shahab Atif, Yong How Choong, Fu YuTao, Weng Zhiping, Liu JianJun, Zhao Xiao Dong, Chew Joon-Lin, Lee Yen Ling, Kuznetsov Vladimir A, Sung Wing-Kin, Miller Lance D, Lim Bing, Liu Edison T, Yu Qiang, Ng Huck-Hui, Ruan Yijun "A global map of p53 transcription-factor binding sites in the human genome." Cell 2006 Jan 13 ; 124(1) : 207-19
Abstract
7. Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin L. Hibberd1, Edison T. Liu, Forest Rohwer, and Yijun Ruan (2006) RNA Viral Community in the Human Gut: Prevalence of plant pathogenic viruses. PLoS Biology 4: Issue 1, e3

8. The FANTOM Consortium, … Yijun Ruan, …, etc (2005) “The Transcriptional Landscape of the Mammalian Genome” Science 309: 1559-1563

9. Patrick Wei Pern NG, Chia Lin WEI, Ken Wing Kin SUNG, Kuo Ping CHIU, Leonard LIPOVICH, Ang Chin Chin, Sanjay GUPTA, Shahab Atif, Wong Chee Hong, Ridwan Azmi, Edison Tak-Bun LIU, Yijun RUAN (2005) "Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation" Nature Method 2 105-111
Supplemental Data File
10. Ruan Yi Jun, Wei Chia Lin, Ee Ai Ling, Vega Vinsensius B, Thoreau Herve, Su Se Thoe Yun, Chia Jer-Ming, Ng Patrick, Chiu Kuo Ping, Lim Landri, Zhang Tao, Peng Chan Kwai, Lin Ean Oon Lynette, Lee Ng Mah, Yee Sin Leo, Ng Lisa F P, Chee Ren Ee, Stanton Lawrence W, Long Philip M, Liu Edison T "Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection." Lancet 2003 May 24 ; 361(9371) : 1779-85