专访NIH赵可吉 3篇Cell首张组蛋白乙酰化图谱

赵可吉博士早年毕业于昌潍师范学院，80年代末赴美，在斯坦福大学接受博士后训练后在NIH任研究员，2007年至今任高级研究员。曾在Cell、Nature、PNAS等权威杂志发表多篇研究性文章，自进入NIH后，开始研究组蛋白乙酰化翻译后调控课题，开发出2套研究组蛋白乙酰化的新技术，在Cell上相继发表3篇乙酰化课题的文章。

　　生物通编者按：2009，已渐行渐远，生命科学的精彩还在继续演绎。一个新的发现可能创造一个全新的研究领域，一个新的发现可能彻底颠覆经典理论，每一位科学家都是生命科学领域的弄潮儿，他或推动着生命科学深刻地变革，或默默填补生命科学认识的鸿沟。2009年，点亮生命之光的是谁？奏响生命之歌的是谁？关注他们，关注赛默飞世尔特约之2009年度生命科学十大风云人物评选！

 

 

乙酰化是一种翻译后的调控方式，近几年，乙酰化的研究十分热门，以乙酰化的调控蛋白为靶位的抗癌药物的设计正在如火如荼的开展，然而，乙酰化调控蛋白靶基因的研究却十分匮乏，这严重阻碍了乙酰化研究临床转化的步伐。

 

现任NIH高级研究员赵可吉博士开发出两套研究乙酰化及其他翻译后修饰的技术，从2007年起，一路乘风破浪，解开乙酰化对基因表达调控的秘密。赵博士在Cell，Nature Genetics等杂志上发表了这些研究成果文章。

 

最近，他又一篇乙酰化研究成果文章发表在了8月份Cell杂志的在线版上。这些成果对未来癌症药物的设计有十分重要的意义。今天，我们走近高级研究员赵可吉博士，随着生物通

记者了解更多。

 

 

赵可吉博士早年毕业于昌潍师专，80年代末赴美，在斯坦福大学接受博士后训练后在NIH任研究员，2007年至今任高级研究员（详细介绍请见文后）。曾在Cell、Nature、PNAS等权威杂志发表多篇研究性文章，自进入NIH后，开始研究组蛋白乙酰化翻译后调控课题，开发出2套研究组蛋白乙酰化的新技术，仅这一课题就在Cell上相继发表3篇文章。

 

生物通：您能简单介绍一下这篇Cell文章的成果吗？

 

赵可吉：我们了绘制真核细胞染色质中的HATs和HDACs综合靶基因全基因组图谱。1. 在人类T细胞中鉴定出5个HATs和4个HDACs全基因组靶位点。2. 证实HDACs不仅仅是转录的辅助抑制子,还能调控染色质中的活性基因。3. 发现 HATs除了与活性记忆有功能上的联系外，还与被抑制的基因在某些程度上有关联。4.研究发现MLL介导的H3 lysine 4甲基化可促进组蛋白乙酰化。5.HDACs主要通过阻止RNA聚合酶Ⅱ与 潜在靶位的结合来抑制转录。

生物通：这篇文章主要发现了什么样的结论，有什么重要的临床意义？

 

赵可吉：这篇文章主要发现，HDACs不仅仅具有抑制转录的功能还能修饰染色质中的活性基因。我们还发现失活的基因首先通过与MLL介导的H3K4甲基化作用，随后接受HAT/HDAC的动态乙酰化和去乙酰化的作用，在阻止基因与PolⅡ结合而抑制基因表达的同时，可以使这些基因保持能够被激活的状态。沉默的基因如果没有接受H3K4的甲基化信号则不能与HDACs结合。

 

在过去几年里，大量临床研究证明HDACs抑制剂是最具有前景的抗癌药物。然而，这类药物抑制癌症细胞的机制却一直不明确，这是科学家们对细胞中HDAC基因功能知识的缺乏所致。我们的研究成果 为抗癌药物的设计提供了新的思路。比如说，先前研究认为HDAC6是存在于细胞质中的。我们的研究数据表明，HDAC6也定位于细胞核染色质中的，并具有调控转录的重要功能。此外，我们的数据显示，很多基因能与多种HATs和HDACs结合，这表明，组蛋白乙酰化的调控十分复杂。这些研究成果有利于未来抗癌药物的设计。

 

生物通：您用什么技术研究HAT/HDAC？在试验中您用什么细胞来研究HAT/HDAC？

 

赵可吉：在这项工作中，我们主要用ChIP-Seq技术研究HATs/HDACs，ChIP-Seq结合了免疫沉淀技术和新一代测序技术，主要用于在全基因组水平上绘制组蛋白修饰图谱，关于这一技术的研究及最初的应用我们发表在Cell和Nature Genetics上的文章里（Cell, 2007; 2008; Nature Genetics, 2008）。ChIP-Seq是一种无偏差的(unbiased)、定量的染色质修饰酶和组蛋白修饰图谱检测技术。

我们主要用人类CD4+ T 细胞做研究模型。

生物通：乙酰基化是一种翻译后修饰机制，它是如何影响基因的沉默或是表达的？

 

赵可吉：乙酰化对基因的表达和沉默的控制至少是通过两套不同的控制机理。比如说，乙酰化可中和组蛋白中赖氨酸残基上的正电荷， 从而使染色质解聚 ，这一变化有助于染色质与调节性因子结合。同时，许多转录调节性酶能够识别染色质上乙酰基，从而结合它们的靶基因而激活这些靶基因的转录。

 

 生物通：乙酰基化作为一种翻译后修饰作用对疾病的研究，尤其是癌症方面有哪些重要的作用？

 

赵可吉：组蛋白乙酰化是一种关键的翻译后修饰模式，对组蛋白，其他蛋白的修饰都具有重要的作用，主要对转录的调节具有重要的意义。一旦编码HATs和HDACs的基因发生突变，将导致多种疾病的发生，包括癌症。以HDACs为靶位设计抑制药物是一种有前景药物设计方式，最近几年，很多抗癌药物和抗其他人类疾病的药物都是这种设计思路。

生物通：您研究组蛋白乙酰化有多长时间了，到目前为止取得了哪些成果？

 

赵可吉：我来到NIH后开始对组蛋白乙酰化调节染色质结构课题感兴趣。然而，这个研究过程的突破点在于我们实验室首次开发了一种无偏差的全基因组图谱测绘技术，我们称为“GMAT”。我们通过这一技术首次绘制了第一张人类T细胞组蛋白乙酰化的全基因组图谱。最近，我们又应用ChIP-Seq技术在全基因组上测定了18个组蛋白乙酰化位点（Nature Genetics，2008）。对这些数据的分析让我们了解更多组蛋白乙酰化对基因表达和基因组结构调节的机制。

 

生物通：作为NIHLBI的高级研究员，您如何看待近年来中国生命科学发展情况？

 

赵可吉：中国这几年在生命科学领域发展迅猛，在表观遗传学和系统生物学方面取得了许 多令人振奋的成果，这得益于很多在海外接受过专业训练的顶尖研究人才的回国工作。我很高兴看到这样的景况。

后记

虽然很忙，但赵老师一丝不苟的帮助我修改文稿，详细到一字一句都推敲。我明白，这对定居海外多年的赵老师来说，并不是容易的事，在此特别感谢赵老师对采访稿的批改。

（生物通 张欢）

 

Curriculum Vitae

 

Keji Zhao, Ph.D.

 

Office Address     Laboratory of Molecular Immunology

                     NHLBI, NIH

                     Building 10, Room 7B06

                     9000 Rockville Pike, MD 20892-1674

                     Tel. [phone];  Fax. [phone]

                     E-mail: [e-mail]

 

Professional Experience

 

2007 --- present          Senior Investigator

Laboratory of Molecular Immunology

                     National Heart, Lung, and Blood Institute

                     National Institutes of Health

 

10/1999---2006             Investigator

                     Laboratory of Molecular Immunology

                     National Heart, Lung, and Blood Institute

                     National Institutes of Health

 

Academic Background

 

1997---1999           Stanford University,

Damon Runyon-Walter Winchel Cancer Research Postdoctoral Fellow

                            Supervisor: Professor Gerald.R. Crabtree

 

1990---1996        University of Geneva, Switzerland

                            graduate student in Molecular Biology

                            obtained Ph.D. degree (1996)

                            Advisor: Professor Ulrich.K. Laemmli

 

1988---1990        Southern Illinois University at Carbondale

                            graduate student in Organic Chemistry

                    

1982---1985        Northeast Normal University, Changchun, China

                            graduate student in Organic Chemistry

                            obtained M.S. degree (1985)

                            Advisor: Professors Yunhong Sun and Huade Pan

 

1978---1980        Changwei Normal College, Weifang, China

                            undergraduate student in Chemistry

                            obtained Diploma in Chemistry

Awards and Other Scientific Recognitions

 

2007               National Institutes of Health Merit Award for “Innovative contributions that have provided novel insights into epigenetic control of gene expression”

 

2008            APAO Award for Significant Accomplishments in Biomedical Research

 

2008            National Institutes of Health Merit Award

 

 

Board and Committees

 

2007                             NIH Director’s Roadmap Project working group

 

2006 to 2007                 NHLBI Technology Transfer Committee

 

2007 to present        NHLBI Promotion and Tenure Committee

 

2007 to present    served in multiple search committees in different institutes at NIH

 

2008 to present            Acting Chair, Steering Committee of NHLBI Genomics Core Facility

 

2009 to present            Member of Steering Committee of NHLBI DNA Sequencing and Computational Biology Core Facility

 

2009                    Editorial Board of Genome Research

 

 

 

 

Selected Publications

 

 

1. Keji Zhao, Emmanuel Kas, Eduardo Gonzalez and Ulrich K. Laemmli (1993), SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. The EMBO J. 12 3237-3247.

 

2. Keji Zhao, Craig M. Hart and Ulrich K. Laemmli (1995), Visualisation of chromosomal domains with boundary element-associated factor BEAF-332. Cell, 81 879-889.

 

3. Craig M. Hart, Keji Zhao and Ulrich K. Laemmli (1997), The scs' boundary-element: characterization of boundary element-associated factors. Molecular and Cellular Biology, 17 999-1009.

 

4. Keji Zhao, Weidong Wang, Oliver J. Rando, Yutong Xue, Kristine Swiderek, Ann Kuo, and Gerald R. Crabtree (1998). Rapid and Phosphoinositol-Dependent Binding of the SWI/SNF-like BAF Complex to Chromatin after T Lymphocyte Receptor Signaling. Cell, 95 625-636.

 

5. Oliver J. Rando, Keji Zhao, and Gerald R. Crabtree (2000). Searching for a

 Function for Nuclear Actin. Trends in Cell Biology, 10 92-97.

 

6. Mimi Wan, Keji Zhao, and Uta Francke (2001). MECP2 truncating mutations cause histone H4 hyperacetylation in Rett syndrome. Human Molecular Genetics, 10 1085-1092.

 

7. Rui Liu, Hong Liu, Xin Chen, Martha Kirby, Patrick O. Brown, and Keji Zhao (2001). Regulation of CSF1 Promoter by the SWI/SNF-like BAF Complex. Cell, 106, 309-318.

 

8. OJ. Rando, K. Zhao, P. Janmey, and GR. Crabtree (2002). Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex. Proc Natl Acad Sci USA, 99, 2824-9.

 

9. Tian Chi, Mimi Wan, Keji Zhao, Ichiro Taniuchi, Chris B. Wilson, and Gerald R. Crabtree (2002). T Lymphocyte Development and Reciprocal Coreceptor Gene Regulaion Require the SWI/SNF-like BAF Chromatin Remodeling Complex. Nature, 418, 195-199.

 

10. Hong Liu, Hyeog Kang, Rui Liu, Xin Chen, and Keji Zhao (2002). Maximal Induction of a Subset of Interferon Target Genes Requires the Chromatin Remodeling Activity of the BAF Complex. Molecular and Cellular Biology, 22, 6471-6479.

 

11.Hong Liu and Keji Zhao (2004). Assays of Z-DNA structure induced by chromatin remodeling enzymes. chapter in Method in Enzymology, Ed. Carl Wu and C. David Allis. Elsevier Science. San Diego. 377, 412-420.

 

12. Hyeog Kang, Kairong Cui, and Keji Zhao (2004). BRG1 controls the activity of the retinoblastoma protein via regulation of p21. Molecular and Cellular Biology, 24, 1188-1199.

 

13. Kairong Cui, Prafullakumar Tailor, Hong Liu, Xin Chen, Keiko Ozato, and Keji Zhao (2004). The Chromatin Remodeling BAF Complex Mediates Cellular Antiviral Activities by Promoter Imprinting. Molecular and Cellular Biology, 24, 4476-4486.

 

14. Tae-Young Roh, Aby Ngau, David Landsman, and Keji Zhao (2004). High-resolution genome-wide mapping of histone modifications.  Nature Biotechnology, 22, 1013-1016.

 

15. Tae-Young Roh, Suresh Cuddapah, and Keji Zhao (2005). Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping.  Genes & Development. 19, 542-552.

 

16. Zhijing Yan, Kairong Cui, Darryl M. Murray, Chen Ling, Yutong Xue, Ramon Parsons, Keji Zhao, and Weidong Wang (2005). Transcriptional selectivity of PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200. Genes & Development. 19,  1662-1667.

 

17. Hong Liu, Niveen Mulholland, Haiqing Fu, and Keji Zhao (2006). Cooperative activity of BRG1 and Z-DNA formation in chromatin remodeling. Molecular and Cellular Biology, 26, 2550-2559.

 

18. Juhong Liu, Zuqin Nie, Fedor Kouzine, Hye-Jung Chung, Keji Zhao, and David Levens (2006). The flux of transcription factors at the c-Myc promoter is managed by a molecular servo. The EMBO Journal 25,  2119-30.

 

19. Tae-Young Roh and Keji Zhao (2006). High-resolution genome-wide mapping of chromatin modifications by GMAT. Methods in Molecular Biology. Ed. Kare Lehmann Nielsen. Humana Press. 387, 95-108.

 

20. Tae-Young Roh, Suresh Cuddapah, Kairong Cui, and Keji Zhao (2006). The landscape of histone modifications in human T cells: H3K4me3 and H3K27me3 reciprocally correlate with gene expression. Proceedings of the National Academy of Sciences. 103, 15782-15787.

 

21. Tae-Young Roh, Gang Wei, Catherine Farrell, and Keji Zhao (2007). Genome-wide prediction of conserved and non-conserved enhancers by histone acetylation patterns. Genome Research. 17,  74-81.

 

22. Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E. Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, and Keji Zhao (2007). High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129, 823-837.

 

23. Beverly Duncan and Keji Zhao (2007). HMGA1 mediates the activation of the CRYAB promoter by BRG1. DNA and Cell Biology 26, 745-52.

 

24. Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E. Schones, Zhibin Wang, Gang Wei, Iouri Chepelev, and Keji Zhao (2007). Response: Mapping nucleosome positions using ChIP-Seq data. Cell 319, 832-833.

 

25. Suresh Cuddapah, Kariong Cui and Keji Zhao (2008). Transcriptional Enhancer Factor 1 (TEF-1/TEAD1) Mediates Activation of IFITM3 Gene by BRG1.  FEBS Letter, 582, 391-397.

 

26. Dustin E. Schones and Keji Zhao (2008). Genome-wide approaches to studying chromatin modifications. Nature Reviews Genetics, 9, 179-191.

 

27. Dustin E. Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei and Keji Zhao (2008). Dynamic regulation of nucleosome positioning in the human genome.  Cell, 132, 887-898.

 

28. Zhibin Wang, Chongzhi Zang, Jeffrey A. Rosenfeld, Dustin E. Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q. Zhang and Keji Zhao (2008). Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics, 40, 897-903.

 

29. Raja Jothi, Suresh Cuddapah, Artem Barski, Kairong Cui and Keji Zhao (2008). Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acid Research, 36, 5221-5231.

 

30. Wei Liao, Dustin E. Schones, Jangsuk Oh, Yongzhi Cui, Kairong Cui, Tae-Young Roh, Keji Zhao and Warren Leonard (2008). Priming for Th2 differentiation requires IL-2-mediated induction of IL-4 receptor a chain expression. Nature Immunology, 9, 1288-1296.

 

31. Anant Jani, Mimi Wan, Jianmin Zhang, Kairong Cui, Jie Wu, Paula Preston-Hurlburt, Rohini Khtri, Keji Zhao, Tian Chi (2008). A novel genetic strategy reveals unexpected roles of the SWI/SNFlike chromatin remodeling BAF complex in thymocyte development. Journal of Experimental Medicine, 205, 2813-2825.

 

32. Suresh Cuddapah Raja Jothi, Dustin E. Schones, Tae-Young Roh, Kairong Cui and Keji Zhao (2009). Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research, 19, 24-32

 

33. Kairong Cui, Chongzhi Zang, Tae-Young Roh, Dustin E. Schones, Richard Childs, Weiqun Peng and Keji Zhao (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate that fate of bivalent genes during differentiation. Cell Stem Cell, 4, 80-93.

 

34. Gang Wei, Lai Wei, Jinfang Zhu, Chongzhi Zang, Jane Hu-Li, Zhengju Yao, Kairong Cui, Yuka Kanno, Tae-Young Roh, Wendy Watford, Dustin E. Schones, Weiqun Peng, Hongwei Sun, William E. Paul, John J. O’Shea*, Keji Zhao*  (2009) Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4⁺ T Cells. Immunity, 30, 155-167. (*co-corresponding authors)

 

35. Jinfang Zhu, Todd S. Davidson, Gang Wei, Dragana Jankovic, Kairong Cui, Dustin E. Schones, Liying Guo, Keji Zhao, Ethan M. Shevach and William E. Paul (2009). Down-regulation of Gfi-1 expression by TGFb is important for Th17 and inducible regulatory T cell differentiation. Journal of Experimental Medicine, 206, 329-41.

 

36. Artem Barski and Keji Zhao (2009) Genomic location analysis by ChIP-Seq. Journal of Cellular Biochemistry, 107, 11-8.

 

37. Deyou Zheng, Keji Zhao, Mark Mehler (2009). Profiling RE1/REST-mediated histone modifications in the human genome. Genome Biology 10: R9.

 

38. Lena Ho, Raja Jothi, Jehnna Ronan, Brett Staahl, Lei Chen, Ann Kuo, Kairong Cui, Alexey Neshvizhskii, Jeff Ranish, Keji Zhao, Gerald R. Crabtree (2008). An Embryonic Stem Cell Chromatin Remodeling Complex, esBAF is an Essential Component of the Core Pluripotency Transcription Network. Proceedings of the National Academy of Sciences. 106, 5187-91.

 

39. Zhibin Wang, Dustin E. Schones and Keji Zhao (2009). Characterization of Human Epigenomes, Current Opinions in Genetics & Development,  19: 127-134.

 

40. Jeffrey A. Rosenfeld, Zhibin Wang, Dustin E. Schones, Keji Zhao, Rob DeSalle, Michael Q. Zhang (2009). Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics, 10, 143.

 

41. Yasuto Araki, Zhibin Wang, Chongzhi Zang, William Wood, III, Dustin Schones, Kairong Cui,Tae-Young Roh, Brad Lhotsky, Robert Wersto, Weiqun Peng, Kevin Becker, Keji Zhao*, and Nan-ping Weng* (2009).Genome-wide analysis of histone methylation reveals a chromatin state based complex regulation of differential gene transcription and function of CD8 memory T cells. Submitted. Immunity, 30, 912-925. (*co-corresponding authors),

 

42. Eric Kallin, Ru Cao, Raja Jothi, Kairong Cui, Keji Zhao and Yi Zhang (2009). Genome wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes, PLoS Genetics, 5, e1000506.

 

43. Chunyuan Jin, Chongzhi Zang,  Keji Zhao*, Gary Felsenfeld* (2009). Chromatin Architecture Organized by Histone Variants H3.3 and H2A.Z in the Human Genome. Nature Genetics, 41, 941-945. (*co-corresponding authors)

 

44. Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui and Keji Zhao, Weiqun Peng (2009). Statistical model for identification of ChIP-enriched regions from ChIP-Seq data. Bioinformatics, 25, 1952-1958.

 

45. Iouri Chepelev, Gang Wei, Qingsong Tang and Keji Zhao (2009). Detection of single nucleotide variations in expressed exons of the human genome. Nucleic Acid Research, in press.

 

46. Zhibin Wang, Chongzhi Zang, Kairong Cui, Dustin E. Schones, Artem Barski, Weiqun Peng and Keji Zhao (2009). Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell, published online August 20, 2009.

 

47. Artem Barski, Raja Jothi, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Dustin E. Schones and Keji Zhao (2009). Chromatin Poises miRNA and Protein-coding Genes for Expression. Genome Research, in press.

 

48. Liying Guo, Gang Wei, Jinfang Zhu, Wei Liao, Warren J. Leonard, Keji Zhao, and William Paul (2009). IL-1 family members and STAT activators induce cytokine production by Th2, Th17, and Th1 cells. Proceedings of the National Academy of Sciences. 106, 13463-8.