Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, China.
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.
- Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, Chen LL. 2015. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev, 29: 630-645.(Highlight by Elbarbary RA and Maquat LEt. Genes Dev, (2015) 29:687¨C689).
- 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, in press.
- Yin QF, Chen LL and Yang L. 2015. Fractionation of non-polyadenylated and ribosomal-free RNAs from mammalian cells. Methods Mol Biol,1206:69-80.
- Yang L and Chen LL. 2014. Microexons go big. Cell, 159:1488-1489.
- Yang L and Chen LL. 2014. Competition of RNA splicing: line in or circle up. Sci China Life Sci, 57:1232-1233.
- Yin QF, Hu SB, Xu YF, Yang L, Carmichael GG and Chen LL. 2014. SnoVectors for nucelar expression of RNA. Nucleic Acids Res, epub on Nov. 5th. pii:gku1050.
- Chen LL and Zhao JC. 2014. Functional study of long noncoding RNAs in development and diseases. Adv Exp Med Biol. 825:129-158.
- Zhang Y, Wang HB and Chen LL. 2014. Circular RNAs: new noncoding RNAs emerging from genome ¡¯dark matter¡¯. Chemistry of Life, 34:428-433.
- 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 highlighted by Nat Rev Genetics, (2014) 15.)
- Zhang Y, Yang L and Chen LL. 2014. Life without A tail: new formats of long noncoding RNAs. Int J Biochem and Cell Biol, 54:338-349.
- Chen LL. 2014. Scientific migration of junior scientists to China. Genome Biol, 15: 119.
- 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)
- 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 highlight by Younger ST and Rinn JL. Cell Res, (2014) 24:643-644; highlighted by Nature.com, by Global Medical Discovery and by National Science Review.)
- 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 highlight by Nature, (2013) 501:464; highlighted by Reid T. Nature China, (2013) epub. on Oct. 2nd (doi:10.1038); by Tomkins J. Institute for Creation Research, (2013) epub. on Oct. 9th.)
- 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.
- Xiang JF, Yin QF and Chen LL. 2013. Long noncoding RNAs: regulatory molecules in mammalian cells. Chin J Cell Biol, 35:262-272.
- 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 highlight by David R. Nat Rev Mol Cell Biol, (2012) 13:686; recommended in F1000 Prime; news coverage in Foundation for Prader-Willi Research. Best of Molecular Cell 2012.)
- Chen LL and Carmichael GG. Nuclear editing of mRNA 3¡¯-UTRs. 2012. Curr Top Microbiol Immunol, 353:111-121.
- Peng S, Chen LL, Lei XX, Yang L, Lin H, Carmichael GG, Huang Y. 2011. Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells, 29:496-504.
- 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 and highly accessed)
- Chen LL and Carmichael GG. 2010. Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol, 22: 357-364.
- 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. (News & Views; preview by Williams BRG. Cell Cycle, (2010) 35:3400.)
- Chen LL and Carmichael GG. 2010. Long non-coding RNAs in mammalian cells: What, Where and Why? WIREs RNA, 1: 2-21.
- 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; recommended in F1000 Prime.)
- 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.
- 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