报告人 ：张强锋 教授，Principle Investigator
主 持 人：屈良鹄教授
报告时间： 2016年3月21日 10:00 AM
RNA structurome reveals the second layer of genetic information
The most remarkable findings in the past two decades in biology include how the mammalian genome is largely transcribed and how versatile functions RNA molecules can have. RNA structure may play a critical role in defining its function and regulation. However, due to lack of information, our knowledge on RNA structural language is very limited. In this talk, I will describe our recent effort in using new chemistry and deep sequencing techniques to probe RNA structures on a genome-wide scale. The study provides both the landscape and also the variation of human and mouse structural transcriptome. Analysis reveals structure features of stable and dynamic elements, long-range interactions, alternative structures, etc., in the context of biological processes including translation, RNA methylation, and RNA-protein interaction etc. Our results demonstrate that by leveraging on the power of next generation sequencing we can now approach to the structural dimension, i.e., the second layer of the complexity of post-transcriptional regulation.
Dr. Qiangfeng ZHANG , Ph.D., is an assistant professor and principle investigator in the Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University. Dr. Zhang received his B.S. and his first Ph.D. from University of Science and Technology of China in 2000 and 2006, respectively, and his second Ph.D. from Columbia University in 2012. He worked as a postdoc at Columbia and Stanford, before he joined Tsinghua in 2015. Dr. Zhang’s research interest focuses on the new area of Structural Systems Biology by combining computational and high-throughput experimental investigations. Dr. Zhang developed a coarse-grained structural modeling method that can accurately and effectively reconstruct protein-protein interaction networks s on a genome-wide scale (Nature 2012, PNAS 2010). Dr. Zhang also developed high-throughput experimental methods to profile in vitro and in vivo structures of the whole transcriptome (Nature 2014, Nature 2015). Dr. Zhang also involved in the development of a technique to identify protein-RNA interactions, a method is specifically useful for the study of non-coding RNA regulation and functions (Cell 2015).
1. Flynn RA*, Zhang QC*, Spitale RC*, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016;11(2):273-90. (*Co-first authorship).
2. Spitale R*, Flynn RA*, Zhang QC*, Pete Crisalli, Byron Lee, Jong-Wha Jung, Hannes Y. Kuchelmeister, Pedro J. Batista, Eduardo A. Torre, Eric T. Kool, and Chang HY. (2015) Structural imprints in vivo decode mechanisms of RNA regulation. Nature. 519 (7544): 486-90. (*Co-first authorship)
3. Chu C, Zhang QC, Texira S, Bharadwaj M, Calabrese M, Magnuson T, Heard H and Chang HY. (2015) Developmentally regulated and modular assembly of Xist RNA binding proteins coordinate chromatin silencing. Cell. 161 (2): 404-16.
4. Wan Y*, Qu K*, Zhang QC, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E and Chang HY. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505 (7485), 706-9.
5. Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive Variation in Chromatin States Across Human Individuals and Populations. (2013) Science 342 (6159), 750-752.
6. Zhang QC, Petrey D, Garzon J, Deng L, and Honig B. (2013) PrePPI: A structure-informed database of protein-protein interactions. Nucleic Acids Research, 41:D828-33.
7. Zhang QC*, Petrey D*, Deng L, Qiang L, Shi Y, Chan AT, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, and Honig B. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 490 (7421): 556-560 (*Co-first authorship)
8. Zhang QC*, Deng L*, Guan J, Honig B and Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. (2011) Nucleic Acids Research, 39: W283-87 (*Co-first authorship)
9. Zhang QC, Petrey D, Norel R, and Honig B, (2010) Protein interface conservation across structural space. Proceedings of the National Academy of Sciences, 107(24): 10896-109