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PHILIPP KAPRANOV, PhD

发布时间:2020-02-25 浏览次数:

 

Philipp Kapranov, Ph.D.

菲利普卡帕诺夫 博士

教授,博士生导师

基因组学研究所所长

福建省百人计划特聘专家

福建省高校领军人才

福建省高端外专团队领军人才

 话:0592-6167250

E-mail: philippk08@hotmail.com

Philipp Kapranov教授长期从事系统生物学和基因组学功能方面的研究,是人类基因组普遍转录概念的提出者之一,他的成果(The Dark Genome)2010年科学杂志评为过去十年最伟大的发现之一(http://www.aaas.org/news/science-breakthroughs-2010-and-insights-decade)Philipp Kapranov教授近年来发表国际高水平论文70余篇,包括NatureScience Cell及其子刊近二十篇,在vlincRNAsncRNAs分子机制、表达水平、功能机制等方面取得了众多显著成果。

Philipp Kapranov教授是ENCODEFANTOM5等国际研究合作联盟的成员,同时兼任NatureGeneGenome BiologyGenome ResearchPNAS Nature Biotechnology Nature Genetics等著名杂志的审稿人。

★欢迎生物、医学、数理统计、计算机专业背景的学生报考硕博士生;也欢迎理工科相关专业学生有此类研究兴趣的跨专业申请。

 

研究领域(Research Area)

Our group combines systems biology, next generation single molecule sequencing and traditional molecular biology to discover the intricacies of molecular processes happening in our cells. Our research interests focus on two main directions:

1.    Characterizing the class of very long intergenic non-coding (vlinc) RNAs recently discovered by us using the combination of approaches mentioned above. Specifically, we are interested in role these RNAs play in cancer and early development.

2.    Development of new methods of transcriptomics and genomics analyzes using the single-molecule sequencing platform enabling novel biological discoveries.

本实验室结合系统生物学、新一代单分子测序以及传统的分子生物学手段,探索人类细胞中复杂的分子生理过程。主要研究方向包括:

1. 本实验室先前已经发现了一组和细胞多能性和癌症相关的vlincRNAs,应用系统生物学、新一代分子测序以及分子生物学方法鉴别vlincRNAs的功能特性。尤其是这类RNAs在癌症以及早期发育中的作用机制。

2. 在单分子测序平台基础上研发新的技术方法,并将其应用于转录组学以及基因组学分析中,解答更多的生物难题。

 

代表性论文(Selected Publications):

1. Xu D, Cai Y, Tang L, Han X, Gao F, Cao H, Qi F, Kapranov P. A CRISPR/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response. Sci Rep. 2020 Feb 4;10(1):1794.

 

2. Wang C, Song J, Liu W, Yao Y, Kapranov P, Sample KM, Gajendran B, Zacksenhaus E, Hao X, Ben-David Y. FLI1 promotes protein translation via the transcriptional regulation of MKNK1 expression. Int J Oncol. 2020 Feb;56(2):430-438.

 

3. Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, Wahlestedt C, Kapranov P. Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. Nat Commun. 2019 Dec 20;10(1):5799.

 

4. Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN. Diversification of Retinoblastoma Protein Function Associated with Cis and Trans Adaptations. Mol Biol Evol. 2019 Dec 1;36(12):2790-2804.

 

5. Diao Y, Rahman MF, Vyatkin Y, Azatyan A, St Laurent G, Kapranov P, Zaphiropoulos PG. (2018) Identification of novel GLI1 target genes and regulatory circuits in human cancer cells. Mol Oncol. 12:1718-1734.

 

6. Cao H, Wahlestedt C, Kapranov P. (2018) Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls. Trends Genet 34:704-721.

 

7. St Laurent G, Vyatkin Y, Antonets D, Ri M, Qi Y, Saik O, Shtokalo D, de Hoon MJ, Kawaji H, Itoh M, Lassmann T, Arner E, Forrest AR; FANTOM consortium, Nicolas E, McCaffrey TA, Carninci P, Hayashizaki Y, Wahlestedt C, Kapranov P. (2016) Functional annotation of the vlinc class of non-coding RNAs using systems biology approach. Nucleic Acids Res. 44:3233-52. doi: 10.1093/nar/gkw162. Epub 2016 Mar 21.

 

8. Pastori C, Kapranov P, Penas C, Peschansky V, Volmar CH, Sarkaria JN, Bregy A, Komotar R, St Laurent G, Ayad NG, Wahlestedt C. (2015) The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation. Proc Natl Acad Sci U S A. 2015 112:8326-31 [Epub ahead of print]

 

9. St Laurent G, Wahlestedt C, Kapranov P. (2015) The Landscape of long noncoding RNA classification. Trends Genet 3:239-51.

 

10. Lazorthes S, Vallot C, Briois S, Aguirrebengoa M, Thuret JY, Laurent GS, Rougeulle C, Kapranov P, Mann C, Trouche D, Nicolas E. (2015) A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nature Communications 6:5971.

 

11. Wang Q, Dong B, Firrman J, Roberts S, Moore AR, Cao W, Diao Y, Kapranov P, Xu R, Xiao W. (2014) Efficient Production of Dual Recombinant Adeno-Associated Viral Vectors for Factor VIII Delivery. Hum Gene Ther Methods 25:261-8.

 

12. St Laurent G, Vyatkin Y, Kapranov P. (2014) Dark matter RNA illuminates the puzzle of genome-wide association studies. BMC Medicine 12:97.

 

13. Villegas VE, Rahman MF, Fernandez-Barrena MG, Diao Y, Liapi E, Sonkoly E, Ståhle M, Pivarcsi A, Annaratone L, Sapino A, Ramírez Clavijo S, Bürglin TR, Shimokawa T, Ramachandran S, Kapranov P, Fernandez-Zapico ME, Zaphiropoulos PG (2014) Identification of novel non-coding RNA-based negative feedback regulating the expression of the oncogenic transcription factor GLI1. Mol Oncol. 8(5):912-26.

 

14. Savva YA, Jepson JE, Chang YJ, Whitaker R, Jones BC, St Laurent G, Tackett MR, Kapranov P, Jiang N, Du G, Helfand SL, Reenan RA (2013) RNA editing regulates transposon-mediated heterochromatic gene silencing. Nature Commun 4:2745

 

 

15. St Laurent G, Shtokalo D, Dong B, Tackett MR, Fan X, Lazorthes S, Nicolas E, Sang N, Triche TJ, McCaffrey TA, Xiao W, Kapranov P (2013) VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer. Genome Biol 14(7):R73. [Epub ahead of print].

 

16. Dong B, Moore AR, Dai J, Roberts S, Chu K, Kapranov P, Moss B, Xiao W. (2013) A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy. Nucleic Acids Res 41(13):6609-17.

 

17. St. Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P (2013) On the Importance of Small Changes in RNA Expression. Methods 63(1): 18-24. [Epub ahead of print].

 

18. St Laurent G, Kapranov P (2013) Genomics in the assessment of a multi-component, multi-target medication in soft tissue disorders. Curr Med Res Opin 29 Suppl 2:11-4.

 

19. St Laurent G 3rd, Shtokalo D, Tackett M, Yang Z, Eremina T, Wahlestedt C, Inchima SU, Seilheimer B, McCaffrey TA, Kapranov P. (2012) Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 13(1):504. [Epub ahead of print]

 

20. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA

elements in the human genome. Nature 489:57-74.

 

21. ENCODE Project Consortium (2012) Landscape of transcription in human cells. Nature 489:101-8.

 

22. Kapranov P, St. Laurent G (2012) Genomic "dark matter": implications for understanding human disease mechanisms, diagnostics, and cures. Front Genet. 3:95. [Epub 2012 May 29].

 

23. St Laurent G, Savva YA, Kapranov P (2012) Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape. Front Genet. 3:57. [Epub 2012 Apr 25].

 

24. Kapranov P, St Laurent G (2012) Dark Matter RNA: Existence, Function, and Controversy. Front Genet. 3:60. [Epub 2012 Apr 23].

 

25. Kapranov P, Chen L, Dederich D, Dong B, He J, Steinmann KE, Moore AR, Thompson JF, Milos PM, Xiao W (2012) Native Molecular State of Adeno-Associated Viral Vectors Revealed by Single-Molecule Sequencing. Hum Gene Ther 23:46-55. [Epub 2011 Oct 4].

 

26. Djebali S*, Lagarde J*, Kapranov  P*, Lacroix  V, Mudge JM, Ucla C, Foissac S, Howald C, Chrast J, Ribeca P, Martin D, Murray RR, Yan X, Ghamsari L, i Lin C, Bell I, Dumais E, Drenkow J, van Berkum  NL, Lajoie BR Vidal M, Stamatoyannopoulos J, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR (2012) Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 7:e28213. [Epub 2012 Jan 4].

*equal contribution.

27. Kapranov P, St. Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorensen PHB, Reaman G, Milos PMM, Arceci RJ, Thompson JF, Triche TJ (2010) The majority of total nuclear-encoded non-ribosomal RNA in a human cell is “dark matter” unannotated RNA. BMC Bio 8:149.

 

28. modENCODE Consortium (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787-97.

 

29. Kapranov P*, Ozsolak F*, Kim SW*, Foissac F*, Huang J, Lipson D, Hart C, Roels S, Borel C, Antonarakis SE, Monaghan AP,  John B, Milos PM (2010) Novel class of human RNA species associated with gene termini suggests an uncharacterized RNA copying mechanism. Nature  466:642-6.

*equal contribution.

 

30. Yang A, Zhu Z, Kettenbach A, Kapranov P, McKeon F, Gingeras TR, Struhl K (2010) Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have indistinguishable DNA-binding profiles in vivo. PLoS ONE 5:e11572.

 

31. Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan P, John B, Milos PMM (2010) Genome-wide Profiling of Polyadenylation Sites by Direct RNA Sequencing. Cell 143: 1018-1029.

 

32. Kapranov P (2009) Studying chromosome-wide transcriptional networks: new insights into disease? Genome Medicine 1: 50

 

33. Kapranov P (2009) From transcription start site to cell biology. Genome Biology 2009, 10: 217. 

 

34. Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project (2009)

Cold Spring Harbor Laboratory: Fejes-Toth K*, Sotirova V, Sachidanandam R, Assaf G, Hannon GJ;

Affymetrix: Kapranov P*, Foissac S, Willingham AT, Duttagupta R, Dumais E, Gingeras TR

 Post-transcriptional processing generates a diversity of 5’-modified long and short RNAs. Nature  457:1028-32.

*equal contribution.

 

35. Djebali S*, Kapranov P*, Foissac S*, Lagarde J*, Reymond A*, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Vidal M, Calvo M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó G (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nature Methods 5: 629-635.  

*equal contribution.

36. ENCODE Project Consortium. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447:799-816.  

 

37. Denoeud F*, Kapranov P*, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. (2007) Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research. 17:746-59.  *equal contribution.

 

38. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-8. [Epub 2007 May 17].

 

39. Kapranov P, Willingham AT, Gingeras TR (2007). Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 8:413-23. (Epub 2007 May 8).

 

40. Kapranov P, Drenkow J,  Cheng J,  Long J, Helt G, Dike S,  Gingeras TR (2005) Examples of Complex Architecture of the Human Transcriptome Revealed by RACE and High Density Tiling Arrays. Genome Research 15: 987-997.

 

41. Cheng J*, Kapranov P*, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Kampa D, Madhavan G, Ghosh S, Bell I, Gerhard DS, Gingeras TR (2005) Transcriptional Maps of 10 Human Chromosomes at 5 Nucleotide Resolution. Science 308: 1149-1154.

*equal contribution.

41. ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-40.

 

42. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.

 

43. Kapranov P, Sementchenko VI, Gingeras TR (2003) Beyond expressison profiling: Next generation uses of high density oligonucleotide arrays. Briefings in Functional Genomics and Proteomics, 2: 47-56.

 

44. Kapranov P, Cawley SE, Drenkow J, Bekiranov S, Strausberg RL, Fodor SPA, Gingeras TR (2002)  Large-Scale Transcriptional Activity in Chromosomes 21 and 22. Science, 296: 916-919.

 

45. Kapranov P, Jensen TJ, Poulsen C, de Bruijn FJ, Szczyglowski K (1999) A protein phosphatase 2C gene, LjNPP2C1, from Lotus japonicus induced during root nodule development. Proc. Natl. Acad. Sci. USA 96: 1738-1743.

期刊审稿人(REVIEW ACTIVITIES):

- Nature

- Gene

- Genome Biology

- Genome Research

- PNAS

- Nature Biotechnology

- Nature Genetics

- Nucleic Acids Research

- Molecular Cancer

- PLOS

- BMC Genomics

- Frontiers

- Scientific reports

期刊编辑(EDITING OF PROFESSIONAL JOURNALS):

Frontiers in Non-Coding RNA
www.frontiersin.org