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Faculty

Members of CAS, CAE
National Outstanding Young Scientists Award
Principal Investigators
 
Address: 320 Yue Yang Road, Shanghai 200031, P.R. China
Tel: 86-21-54920000
Fax: 86-21-54921011
Email: sibcb@sibs.ac.cn
Website: www.sibcb.ac.cn
 
Principal Investigators
 
CHEN Lingling
Ph.D., Professor
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China.
Email: linglingchen@@sibcb.ac.cn
Lab homepage: www.chenlab-ncrna.com

Research Interests
The complete sequence of the human genome provided quite a surprise to many by revealing that more than 98% of the transcriptional output represents non-protein coding RNAs (ncRNAs). In addition to housekeeping ncRNAs (rRNAs, tRNAs, etc.) and small RNAs (microRNAs, piRNAs, etc.), long noncoding RNAs (lncRNAs, >200nt) are emerging as a major class of eukaryotic transcripts with both reported and yet undiscovered roles in gene regulation.
Our long-term goal is to discover new regulatory RNA species and to study their biogenesis and their mechanisms of action in mammalian cells. In the next five years, we are particularly interested in the following areas.
1) Identify new RNA species in mammalian genomes by taking advantage of genome-wide approaches and computational analyses.
2) Explore their biogenesis and new modes of gene expression regulation by these RNA transcripts with molecular/cell biological and biochemical approaches.
3) Understand the regulatory roles of particular lncRNAs in nuclear architecture and function by genome editing and cell images.
4) Investigate the function of evolutionarily non-conserved lncRNAs by using of human embryonic stem cells as models and gain insights into their regulatory roles in the early development in primates.
Together, these studies have the potential to advance our understanding of the mechanisms and functional roles of lncRNA regulation in human genome.

Selected Publications

  1. Xiang JF#, Yang Q#, Liu CX#, Wu M, Chen LL* and Yang L*. 2018. N6-methyladenosines modulate A-to-I RNA editing. Mol Cell, 69:126-135.
  2. Yang L* and Chen LL*. 2017. Enhancing the RNA engineering tool kit. Science, 358: 996-997.
  3. Li X#, Liu CX#, Xue W#, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L* and Chen LL*. 2017. Coordinated circRNA biogenesis and function with NF90/NF110 in viral infection. Mol Cell, 67: 214-222. (Free featured article; highlighted by Editor¨s Note and Meet the Author; preview by Cadena CY and Hur S. Mol Cell, 2017, 67:163-164.)
  4. Wu H, Yang L*, Chen LL*. 2017. The diversity of long noncoding RNAs and their generation. Trends Genet, 33:540-552.
  5. Xing YH#, Yao RW#, Zhang Y#, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL*. 2017. SLERT regulates DDX21-rings associated with Pol I transcription. Cell, 169: 664-678. (Research highlights by Bull Chin Acad Sci, 2017, 31:152-155.)
  6. Dong R#, Ma XK#, Chen LL* and Yang L*. 2017. Increased complexity of circRNA expression during species evolution. RNA Biol, 14:1064-1074.
  7. Chen LL* and Yang L*. 2017. AlUternative regulation for gene expression. Trends Cell Biol, 27:480-490.
  8. Wu H#, Yin QF#, Luo Z#, Yao RW, Zheng CC, Zhang J, Xiang JF, Yang L and Chen LL*. 2016. Unusual processing generates SPA lncRNAs that sequester multiple RNA binding proteins. Mol Cell, 64:435-437. (Cover story and Issue highlights; preview by Li Y and Fox AH. Mol Cell, 2016, 64:435-437.)
  9. Xing YH#, Bai ZQ#, Liu CX, Hu SB, Ruan MH and Chen LL*. 2016. Research progress of long noncoding RNA in China. IUBMB Life, 68:887-893.
  10. Hu SB, Yao RW and Chen LL*. 2016. Shedding light on paraspeckle structure by super-resolution microscopy. J Cell Biol, 214:789-791.
  11. Chen LL*. 2016. Linking long noncoding RNA localization and function. Trends Biochem Sci, 41:761-772. (Series: Fresh Perspectives from Emerging Experts)
  12. Zhang XO#, Dong R#, Zhang Y#, Zhang JL, Luo Z, Zhang J, Chen LL*and Yang L*. 2016. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 26: 1277-1287.
  13. Zhang Y#, Xue W#, Li X, Zhang J, Zhang JL, Yang L* and Chen LL*. 2016. The biogenesis of nascent circular RNAs. Cell Rep, 15:611-624.
  14. Chen LL*. 2016. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol, 17:205-211. (Cover story)
  15. Zhang Y, Yang L and Chen LL*. 2016. Characterization of circular RNAs. Methods Mol Biol, 1402:215-27.
  16. Xiang JF, Yang L and Chen LL*. 2015. The long noncoding RNA regulation at the MYC locus. Curr Opin Genet Dev, 33:41-48.
  17. Chen LL* and Yang L*. 2015. Gear up in circles. Mol Cell, 58:715-717.
  18. Chen LL* and Yang L*. 2015. Regulation of circRNA biogenesis. RNA Biol, 12:381-388.
  19. Hu SB, Xiang JF, Li X, Xu YF, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D* and Chen LL*. 2015. Protein arginine methyltransferase CARM1 attenuates the nuclear retention of mRNAs containing IRAlus at paraspeckles. Genes Dev, 29: 630-645. (Perspectives by Elbarbary RA and Maquat LE, Genes Dev, 2015, 29:687C689; research highlights by Bull Chin Acad Sci, 2015, 29:108)
  20. Chen T#, Xiang JF#, Zhu S#, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L* and Chen LL*. 2015. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res, 25:459-476.
  21. Yin QF#, Hu SB#, Xu YF, Yang L, Carmichael GG and Chen LL*. 2015. SnoVectors for nuclear expression of RNA. Nucleic Acids Res, 43(1):e5.
  22. Yang L* and Chen LL*. 2014. Microexons go big. Cell, 159:1488-1489.
  23. Zhang XO#, Wang HB#, Zhang Y, Lu X, Chen LL* and Yang L*. 2014. Complementary sequence- mediated exon circularization. Cell, 159:134-147. (Featured article; preview by Vicens Q and Westhof E, Cell, 2014,159:13-14; research highlights by Nat Rev Genetics, 2014, 15:717; F1000 Prime recommendation and Bull Chin Acad Sci, 2014, 28:282-284)
  24. Zhang Y, Yang L and Chen LL*. 2014. Life without A tail: new formats of long noncoding RNAs. Int J Biochem Cell Biol, 54:338-349.
  25. Zhang XO #, Yin QF #, Wang HB, Zhang Y, Chen T, Zheng P, Lu X, Chen LL* and Yang L*. 2014. Species-specific alternative splicing leads to unique expression of sno-lncRNAs. BMC Genomics, 15:287. (Highly accessed; featured article in Biome)
  26. Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wang HB, Ge JH, Lu XH, Yang L and Chen LL*. 2014. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions in the MYC locus. Cell Res, 24:513-531. (Cover article; research highlights by Younger ST and Rinn JL. Cell Res, 2014, 24:643-644; research highlights by Nature.com, Global Medical Discovery and National Science Review, 2015, 2:7-8.)
  27. Chen LL* and Zhao JC*. 2014. Functional study of long noncoding RNAs in development and diseases. Adv Exp Med Biol, 825:129-158.
  28. Zhu S#, Xiang JF#, Chen T, Chen LL* and Yang L*. 2013. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. BMC Genomics, 14:206.
  29. Zhang Y#, Zhang XO#, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L* and Chen LL*. 2013. Circular intronic long noncoding RNAs, Mol Cell, 51: 792-806. (Preview by Bolisetty MT and Graveley BR. Mol Cell, 2013, 51:705-706; research highlights by Nature, 2013, 501:464, Nature China, 2013, doi:10.1038; the most- downloaded article of the month in Mol Cell)
  30. Yin QF#, Yang L#, Zhang Y, Xiang JF, Wu YW, Carmichael GG* and Chen LL*. 2012. Long noncoding RNAs with snoRNA ends. Mol Cell, 48: 219-230. (Cover article; preview by McCann KL and Baserga SJ. Mol Cell, 2012, 48:155-7; research highlights by Nat Rev Mol Cell Biol, 2012, 13:686; F1000 Prime recommendation; news coverage in Foundation for Prader-Willi Research; Best of Mol Cell 2012)
  31. Yang L, Duff MO, Graveley BR, Carmichael GG and Chen LL*. 2011. Genomewide characterization of non- polyadenylated RNAs. Genome Biol, 12: R16. (Editor's pick; highly accessed)
  32. Chen LL* and Carmichael GG. 2010. Long non-coding RNAs in mammalian cells: What, Where and Why? WIREs RNA, 1: 2-21.
  33. Chen LL* and Carmichael GG*. 2010. Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol, 22: 357-364.
  34. Chen LL*, Yang L and Carmichael GG*. 2010. Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells. Cell Cycle, 9:3552-3564. (Research highlights by Williams BRG. Cell Cycle, 2010, 35:3400)
  35. Chen LL and Carmichael GG. 2009. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell, 35: 467-478. (Preview by Scadden D. (2009) Mol Cell, 35:395-396; F1000 Prime recommendation)
  36. Chen LL and Carmichael GG. 2008. Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle, 7: 3297-3301.
  37. Chen LL, Decerbo JN and Carmichael GG. 2008. Alu element-mediated gene silencing. EMBO J, 27: 1694-1705.

Education Background & Academic Experience
2011-present Principal Investigator, Institute of Biochemistry and Cell Biology, SIBS, CAS
2010-2011 Assistant Professor in residence, University of Connecticut Health Center, USA
2009-2010 Post-Doc fellow, University of Connecticut Stem Cell Institute, USA (Supported by Connecticut Stem Cell Seed Award, PI/Ling-Ling Chen)
2007-2009 M.B.A., University of Connecticut, USA.
2004-2009 Ph.D., University of Connecticut, USA.
2000-2003 M.S., Shanghai Institute of Materia Medica, CAS
1996-2000 B.S., Lanzhou University

Research Team

 

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