Publications

2021:

  • 71. Yao RW, Luan PF and Chen LL. 2021. An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies. RNA, 2021 Apr 12;rna.078671.120.
  • 70. Guo SK, Nan F, Liu CX, Yang L and Chen LL. 2021. Mapping circular RNA structures in living cells by SHAPE-MaP. Methods, 2021 Feb 9;S1046-2023(21)00023-2.

2020:

  • 69. Statello L, Guo CJ, Chen LL and Huarte M. 2020. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol, 2021 Feb;22(2):96-118.
  • 68. Li SQ, Li X, Xue W, Zhang L, Yang LZ, Cao SM, Lei YN, Liu CX, Guo SK, Shan L, Wu M, Tao X, Zhang JL, Gao X, Zhang J, Wei J, Li JS, Yang L and Chen LL. 2020. Screening for functional circular RNAs using the CRISPR-Cas13 system. Nat Methods, 2021 Jan;18(1):51-59.
  • 67. Guo CJ, Xu G and Chen LL. 2020. Mechanisms of Long Noncoding RNA Nuclear Retention. Trends Biochem Sci, 45(11):947-960. AOP doi: 10.1016/j.tibs.2020.07.001.
  • 66. Wang Y and Chen LL. 2020. Organization and function of paraspeckles. Essays Biochem, AOP doi: 10.1042/EBC20200010.
  • 65. Wang Y, Yang LZ and Chen LL. 2020. Protocol for Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 System. Star Protocols, AOP doi.org/10.1016/j.xpro.2020.100037.
  • 64. Chen LL. 2020. The expanding landscape of the regulation and functions of circular RNAs. Nat Rev Mol Cell Biol. 21(8):475-490. AOP May 04, 2020.
  • 63. Ma XK, Guo CJ, Yang L and Chen LL. 2020. Altered processing of lncRNA in stem cells contributes to non-conserved functions. Chemistry of Life, 2020. 40(7): 985-991
  • 62. Guo CJ, Ma XK, Xing YH, Zheng CC, Xu YF, Shan L, Zhang J, Wang SH, Wang YM, Carmichael GG, Yang L and Chen LL. 2020. Distinct processing of lncRNAs contributes to non-conserved functions in stem cells. Cell, 181(3):621-636. doi:10.1016/j.cell.2020.03.006
    • Preview by Sharma H and Carninci P, Cell, 2020, 181(3):512-514
  • 61. Yao RW, Liu CX and Chen LL. 2020. Linking RNA processing and function. Cold Spring Harb Symp Quant Biol, AOP doi:10.1101/sqb.2019.84.039495
  • 60. Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O’ Reily D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL and Bruford EA. 2020. A guide to naming human non-coding RNA genes. EMBO J, AOP https://doi.org/10.15252/embj.2019103777
  • 59. Yang LZ, Wang Y and Chen LL. RNA imaging in living cells by CRISPR-Cas13 systems. Chemistry of Life. 2020. 40(1): 1-7
    • Cover Article

2019:

  • 58. Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L. 2019. CIRCexplorer3: A CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics,17(5):511–521. pii:S1672-0229(19)30166-4.
  • 57. A Conversation with Ling-Ling Chen, interviewed by Steve Mao, Senior Editor at Science. 2019. Cold Spring Harb Symp Quant Biol, doi:10.1101/sqb.2019.84.039032
  • 56. Dong R, Ma XK, Chen LL and Yang L. 2019. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline. Methods Mol Biol, 1870:137–149. doi:10.1007/978-1-4939-8808-2_10
  • 55. Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Gordon G. Carmichael, Chen LL. 2019. Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell, 76(6):981-997. doi: 10.1016/j.molcel.2019.10.024.
    • F1000 Prime recommendation
    • Spotlighted by Davis BJ and O’Connell MR, Mol Cell, 2020, 77:207-209
  • 54. Yao RW, Xu G, Wang Y, Shan L, Luan PF, Wang Y, Wu M, Yang LZ, Xing YH, Yang L, Chen LL. 2019. Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus. Mol Cell, 76(5):767-783. pii: S1097-2765(19)30630-6. doi: 10.1016/j.molcel.2019.08.014. (Featured Article)
    • Featured Article and Issue highlights
    • Preview by Lafontaine DL, Mol Cell, 2019, 177(4):797-799
    • Research highlights by Nat Chem Biol, 2019, 15:1029
  • 53. Liu CX, Li X, Nan F and Chen LL. Circular RNAs in innate immunity. Chemistry of Life. 2019, Volume 39, Issue 3, Pages 424-429.
  • 52. Yao RW, Wang Y and Chen LL. Cellular functions of long noncoding RNAs. Nat Cell Biol. 2019 May; 21(5): 542-551. doi: 10.1038/s41556-019-0311-8.
    • Editorial by Nat Cell Biol. 2019, 21:535 (A focus on regulatory RNA)
  • 51. Liu CX, Li X, Nan F, Jiang S, Gao X, Guo SK, Xue W, Cui Y, Dong K, Ding H, Qu B, Zhou Z, Shen N, Yang L and Chen LL. Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell. 2019 May 2;177(4):865-880.e21. doi: 10.1016/j.cell.2019.03.046.
    • Preview by Wilusz JE, Cell, 2019, 177(4):797-799
    • Research Highlighted by: Nat Rev Immunol. 2019, 19:351
    • Research Highlighted by: Nat Rev Mol Cell Biol. 2019, 20:387
    • Research Highlighted by: Science. 2019, 364: 847
    • Research Highlighted by: Cell Bioscience. 2019, 9:43-45
    • Research Highlighted by: Bull Chin Acad Sci. 2019, 33:91-95.
    • Five Recommendations in F1000 Prime
    • News reports by Science News Magazine (https://www.sciencenews.org/article/lack-circular-rna-may-trigger-lupus) by LUPUS NEWS, Technologytimes, Medical Xpress

2018:

  • 50. Xing YH and Chen LL. Processing and roles of snoRNA-ended long noncoding RNAs. Crit Rev Biochem Mol Biol. 2018 Sep 25:1-11. doi: 10.1080/10409238.2018.1508411.
  • 49.Wang Y, Hu SB, Wang MR, Yao RW, Wu D, Yang L, Chen LL. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nat Cell Biol. 2018 Oct; 20(10):1145-1158. doi: 10.1038/s41556-018-0204-2.
    • News and Views by Fox AH, Nat Cell Biol, 2018, 20(10): 1108-1109
  • 48.Li X, Yang L and Chen LL. The Biogenesis, Functions, and Challenges of Circular RNAs. Mol Cell. 2018 Aug; 71(3):428-442. doi: 10.1016/j.molcel.2018.06.034.
  • 47. Xiang JF, Yang Q, Liu CX, Wu M, Chen LL and Yang L. N6-Methyladenosines Modulate A-to-I RNA Editing. Mol Cell. 2018 Jan; 69(1):126-135.e6. doi: 10.1016/j.molcel.2017.12.006.

2017:

  • 46. Liang D, Tatomer DC, Luo Z, Wu H, Yang L, Chen LL, Cherry S, Wilusz JE. The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting. Mol Cell. 2017 Dec; 68(5): 940-954.e3. doi: 10.1016/j.molcel.2017.10.034.
  • 45. Yang L and Chen LL. Enhancing the RNA engineering toolkit. Science. 2017, Nov; 358:6366, 996-997, doi: 10.1126/science.aar2400
  • 44.Wu H, Yang L, Chen LL.The Diversity of Long Noncoding RNAs and Their Generation. Trends Genet. 2017, July; 33(8), 540-552. doi: http://dx.doi.org/10.1016/j.tig.2017.05.004
  • 43. Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Mol Cell. 2017, July; 67(2) 214-277. doi: http://dx.doi.org/10.1016/j.molcel.2017.05.023 (Featured Article)
    • Free featured article
    • Highlighted by Editor's Note and Meet the Authors
    • Preview by Cadena CY and Hur S, Mol Cell, 2017, 67:163-164
  • 42. Xing YH, Yao RW, Zhang Y, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL. SLERT regulates DDX21-rings associated with Pol I transcription. Cell. 2017, 169(4): 664-678.e16. doi: 10.1016/j.cell.2017.04.011.
    • Research highlights by Bull Chin Acad Sci, 2017, 31:152-155
  • 41. Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen LL, Wang Y, Wong CC, Xiao X, Wang Z. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 2017 May; 27(5):626-641. doi: 10.1038/cr.2017.31.
  • 40. Dong R, Ma XK, Chen LL and Yang L. Increased complexity of circRNA expression during species evolution. RNA Biol, 2016 Dec 16:1-11. doi: 10.1080/15476286.2016.1269999.
  • 39. Chen LL, Yang L. ALUternative Regulation for Gene Expression. Trends Cell Biol. 2017, Feb; doi.org/10.1016/j.tcb.2017.01.002.
  • 38. Niu NN, Xiang JF, Yang Q, Wang LJ, Wei ZY, Chen LL, Yang L, Zhou WG. RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression. Cell Discovery, 2017 Jan 24;3:16050. doi: 10.1038/celldisc.2016.50.

2016:

  • 37. Zhang Y, Yang L, Chen LL. Characterization of Circular RNAs. Methods Mol Biol, 2016;1402:215-227. doi: 10.1007/978-1-4939-3378-5_17.
  • 36. Wu H, Yin QF, Luo Z, Yao RW, Zheng CC, Zhang J, Xiang JF, Yang L, Chen LL. Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Mol Cell, 2016 Nov 3;64(3):534-548. doi: 10.1016/j.molcel.2016.10.007.
    • Cover story and Issue highlights
    • Preview by Li Y and Fox AH, Mol Cell, 2016, 64:435-437
  • 35. Chen LL, Claw KG, Ramachandran S. A two-fold challenge: the experience of women of color in genomics. Genome Biol. 2016 Oct 11;17(1):210. doi: 10.1186/s13059-016-1075-0
  • 34. Xing YH, Bai ZQ, Liu CX, Hu SB, Ruan MH, Chen LL. Research progress of long noncoding RNA in China. IUBMB Life. 2016 Oct 3; 68(11):887-893. doi: 10.1002/iub.1564
  • 33. Hu SB, Yao RW, Chen LL. Shedding light on paraspeckle structure by super-resolution microscopy. J Cell Biol. 2016 Sep 26;214(7):789-91. doi: 10.1083/jcb.201609008.
  • 32. Chen LL. Linking Long Noncoding RNA Localization and Function. Trends Biochem Sci. 2016 Sep;41(9):761-72. doi: 10.1016/j.tibs.2016.07.003.
    • Series: Fresh Perspectives from Emerging Experts
  • 31. Chen LL. Ling-Ling Chen: Linking Long Noncoding RNA Processing and Function to RNA Biology. Trends Biochem Sci. 2016 Sep;41(9):733-4. doi: 10.1016/j.tibs.2016.07.006.
  • 30. Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL and Yang L#. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 2016 Sep;26(9):1277-87. doi: 10.1101/gr.202895.115.
  • 29. Zhang Y, Xue W, Li X, Zhang J, Chen S, Zhang JL, Yang L# and Chen LL. The Biogenesis of Nascent Circular RNAs. Cell Rep, 2016 Apr 19;15(3):611-24. doi: 10.1016/j.celrep.2016.03.058.
  • 28. Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL and Yang L. CircRNA-derived pseudogenes. Cell Res, 2016 Jun;26(6):747-50. doi: 10.1038/cr.2016.42.
  • 27. Chen LL. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol, 2016 Feb; 17, 205–211, doi:10.1038/nrm.2015.32.
  • 26. Zhang Y, Yang L and Chen LL. Characterization of Circular RNAs. Methods in Molecular Biology, 2016, Jan; 1402: 215-227(Book chapter)

2015:

  • 25. Xiang JF, Yang L, Chen LL. The long noncoding RNA regulation at the MYC locus. Curr Opin Genet Dev 2015 Aug;33:41-8. doi: 10.1016/j.gde.2015.07.001.
  • 24. Zhong CQ, Yin Q, Xie ZF, Bai MZ, Dong R, Tang W, Xing YH,Zhang HL, Yang SM, Chen LL, Bartolomei MS, Smith AF, Li DS, Yang L, Wu YX, Li JS. CRISPR-Cas9-Mediated Genetic Screening in Mice with Haploid Embryonic Stem Cells Carrying a Guide RNA Library. Cell Stem Cell, 2015 Aug 6;17(2):221-32. doi: 10.1016/j.stem.2015.06.005.
  • 23. Chen LL and Yang L. Gear up in circles. Mol Cell, 2015 Jun 4;58(5):715-7. doi: 10.1016/j.molcel.2015.05.027.
  • 22. Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, and Chen LL. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes & Dev, 2015, 29: 630-645
    • Perspectives by Elbarbary RA and Maquat LE, Genes Dev, 2015, 29:687-689
    • Research highlights by Bull Chin Acad Sci, 2015, 29:108
  • 21. Chen LL and Yang L. Regulation of circRNA biogenesis. RNA Biology, 12:4, 381-388, DOI: 10.1080/15476286.2015.1020271
  • 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, 2015 Apr;25(4):459-76. doi: 10.1038/cr.2015.24.
    • Highlighted by ESC&Ipsc NEWS
  • 19. Yin QF, Hu SB, Xu YF, Yang L, Carmichael GG and Chen LL. SnoVectors for nuclear expression of RNA. Nucleic Acids Res, 2015 Jan;43(1):e5. doi: 10.1093/nar/gku1050.
  • 18. Yin QF, Chen LL and Yang L. Fractionation of Non-polyadenylated and Ribosomal-free RNAs from Mammalian Cells. Methods Mol Biol, 2015, 1206: 69-80 (Book chapter)

2014:

  • 17. Yang L and Chen LL. Microexons go big. Cell, 2014 Dec 18;159(7):1488-9. doi: 10.1016/j.cell.2014.12.004.
  • 16. Yang L and Chen LL. Competition of RNA splicing: line in or circle up. Sci China Life Sci,2014 Dec;57(12):1232-3. doi: 10.1007/s11427-014-4770-7.
  • 15. Zhang Y, Wang HB and Chen LL. Circular RNAs: new noncoding RNAs emerging from genome 'dark matter'. Chemistry of Life, 2014, 34:428-433.
  • 14. Chen LL and Zhao JC. 2014. Functional study of long noncoding RNAs in development and diseases. Adv Exp Med Biol. 825:129-158.
  • 13. Zhang XO, Wang HB, Zhang Y, Lu X, Chen LL and Yang L. Complementary sequence-mediated exon circularization. Cell, 2014, 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
    • Research highlights by Bull Chin Acad Sci, 2014, 28:282-284
    • F1000 Prime recommendation
  • 12. Zhang Y, Yang L and Chen LL. Life without A tail: new formats of long noncoding RNAs. Int J Biochem and Cell Biol, 2014 Sep;54:338-49. doi: 10.1016/j.biocel.2013.10.009.
  • 11. Zhang XO, Yin QF, Chen LL and Yang L. Gene expression profiling of non-polyadenylated RNA-seq across species. Genomics Data,2014 Aug 3;2:237-41. doi: 10.1016/j.gdata.2014.07.005. eCollection 2014 Dec.
  • 10. Chen LL. 2014. Scientific migration of junior scientists to China. Genome Biol, 2014 Jun 24;15(6):119. doi: 10.1186/gb4180.
  • 9. Zhang XO, Yin QF, Wang HB, Zhang Y, Chen T, Zheng P, Lu X, Chen LL and Yang L. Species-specific alternative splicing leads to unique expression of sno-lncRNAs. BMC Genomics, 2014, 15: 287 (Highly Accessed)
    • Highly accessed; featured article in Biome
  • 8. Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wu Z, Zhang S, Wang HB, Ge JH, Lu XH, Yang L and Chen LL. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions in the MYC locus. Cell Res,2014 May;24(5):513-31. doi: 10.1038/cr.2014.35.(Cover Article and Issue Highlight)
    • Research highlights by Younger ST and Rinn JL, Cell Res, 2014, 24:643-644
    • Research highlights by Nature.com
    • Research highlights by Global Medical Discovery
    • Research highlights by National Science Review, 2015, 2:7-8

2013:

  • 7. Xiang JF, Yin QF and Chen LL. Long noncoding RNAs: regulatory molecules in mammalian cells. Chin J Cell Biology, 2013, 35:262-272.
  • 6. Zhang Y, Zhang XO, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L and Chen LL. Circular intronic long noncoding RNAs. Mol Cell, 2013 Sep 26;51(6):792-806. doi: 10.1016/j.molcel.2013.08.017. (Issue Highlight)
    • Preview by Bolisetty MT and Graveley BR, Mol Cell, 2013, 51:705-706
    • Research highlights by Nature, 2013, 501:464
    • Research highlights by by Nature China, 2013, doi:10.1038
  • 5. Zhu S, Xiang JF, Tian C, Chen LL and Yang L. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. BMC Genomics, 2013 Mar 27;14:206. doi: 10.1186/1471-2164-14-206.(Highly Accessed)

2012:

  • 4. Yin QF, Yang L,Zhang Y, Xiang JF, Wu YW, Carmichael GG and Chen LL. Long noncoding RNAs with snoRNA ends. Mol Cell, 2012 Oct 26;48(2):219-30. doi: 10.1016/j.molcel.2012.07.033. (Cover Article and Issue Highlight)
    • Preview by McCann KL and Baserga SJ, Mol Cell, 2012, 48:155-7
    • Research highlights by Nat Rev Mol Cell Biol, 2012, 13:686
    • Five recommendations in F1000 Prime
    • News coverage in Foundation for Prader-Willi Research
    • Best of Molecular Cell 2012
  • 3. Chen LL# and Carmichael GG. Nuclear editing of mRNA 3'-UTRs. 2012. Curr Top Microbiol Immunol, 353:111-121.

2011:

  • 2. 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, 2011 Mar;29(3):496-504. doi: 10.1002/stem.591.
  • 1. Yang L, Duff MO, Graveley BR, Carmichael GG and Chen LL#. 2011. Genomewide characterization of non-polyadenylated RNAs. Genome Biol, 2011;12(2):R16. doi: 10.1186/gb-2011-12-2-r16.
    • Editor's pick and highly accessed

Selected publications before Chen Lab:

  • 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.

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