PANDORA-Seq & the expanding universe of small RNAs
Genetic & environmental control of the 'sperm RNA code'
Epigenetic inheritance through sperm RNAs & RNA modifications
Featured publications
Tracing the celluar & molecular origins of heterogeneity and  symmetry-breaking in mamalian early embryo
Ideas that may spark......
tsRNA origin, evolution & functional principles
Darwin’s pangenesis
       Complete publication list in PubMed or Google Scholar or Researchgate
       Find our papers by keywords:

        Selected Publications (*equal contribution. #correspondence author)

             (2/2023-present) [Associate Professor, University of Utah]

  • Cai C, Chen Q#. Father’s diet influences son’s metabolic health through sperm RNA. Nature (2024) [Journal] [PDF] [News]
  • Wang X, Yu D, Yu J, Hu H,Hang R, Amador Z, Chen Q, Chai J, Chen X#. Toll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity. Nature Communications (2024) [Journal] [PDF]
  • Kuhle B, Chen Q, Schimmel P#. tRNA Renovatio: Rebirth through fragmentation. Molecular Cell (2023) Nov 16;83(22):3953-3971. [Journal] [PDF]
  • Chen Q#, Zhou T#. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. Journal of Biological Chemistry (2023) 299(10) 105225. [Journal] [PDF][tRNA thematic series]
  • Holmes AD, Chan PP, Chen Q, Ivanov P, Drouard L, Polacek N, Kay MA, Lowe TM#. A standardized ontology for naming tRNA-derived RNAs based on molecular origin. Nature Methods (2023) doi:10.1038/s41592-023-01813-2 [Journal] [PDF]
  • Zhang X, Chen Q#. EDC exposure in 3D genome memory in transgenerational obesity. Nature Reviews Endocrinology (2023) [Journal] [PDF] 
    (2/2019-2/2023)  [Assistant Professor - Associate Professor, University of California, Riverside]
  • Chen Q#. Sperm RNA-mediated epigenetic inheritance in mammals: challenges and opportunities. Reproduction, Fertility and Development (2022) doi:10.1071/RD22218 [Journal] [PDF]

  • Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z#. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development (2022) Nov 1;149(21):dev200819. doi: 10.1242/dev.200819 [Journal] [PDF]
  • Shi J, Zhou T#, Chen Q#. Exploring the expanding universe of small RNAs. Nature Cell Biology (2022) Apr;24(4):415–423. doi: 10.1038/s41556-022-00880-5 [Journal] [PDF] (cover story)
  • Yuan X, Su Y, Zhang X, Turkel SJ, Shi S, Wang X, Choi EJ, Wu W, Liu H, Viner R, Russo JJ, Li W, Bao X, Chen Q, Zhang S#. MLC-Seq: de novo Sequencing of Full-Length tRNAs and Quantitative Mapping of Multiple RNA Modifications. Preprint (2021) [Link]
  • Chen Q#, Zhang X, Shi J, Yan M, Zhou T#. Origins and evolving functionalities of tRNA-derived small RNAs. Trends in Biochemical Sciences (2021) Oct;46(10):790-804. [Journal] [PDF]
  • Liu C, Liu H, Zhang H, Wang L, Li M, Cai F, Wang X, Wang L, Zhang R, Yang S, Liu W, Liang Y, Wang L, Song X, Su S, Gao H, Jiang J, Li J, Luo M, Gao F, Chen Q, Li W#, Chen ZJ#. Paternal USP26 mutations raise Klinefelter syndrome risk in the offspring of mice and humans. The EMBO Journal  (2021) May 12;e106864. doi: 10.15252/embj.2020106864 [Journal] [PDF]
  • Shi J*, Zhang Y*, Tan D*, Zhang X*, Yan M*, Zhang Y*, Franklin R*, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S#, Zhang Y#, Zhou T#, Chen Q#. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature Cell Biology  (2021) Apr;23(4):424-436. DOI: 10.1038/s41556-021-00652-7 [Journal] [PDF] [Twitter digest] [News story]
  • Qu Y*, Chen Q*, Guo S*, Ma C, Lu Y, Shi J, Liu S, Zhou T, Noda T, Qian J, Zhang L, Zhu X, Lei X, Cao Y, Li W, Li W, Plachta N, Matzuk MM, Ikawa M, Duan E#, Zhang Y#, Wang H#. Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization. Protein & Cell (2021) doi:10.1007/s13238-021-00825-y [Journal] [PDF] [Movies]
  • Gu W#,*, Shi J*, Liu H*, Zhang X*, Zhou JJ, Li M, Zhou D, Li R, Lv J, Wen G, Zhu S, Qi T, Li W, Wang X, Wang Z, Zhu H, Zhou C, Knox KS, Wang T, Chen Q#, Qian Z#, Zhou T#. Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer. Molecular Cancer. 2020 Nov 12;19(1):159. [Journal] [PDF]
  • Zhang X*, Trebak F*, Souza LA; Shi J, Zhou T, Kehoe PG, Chen Q#, Feng Earley Y#. Small RNA modifications in Alzheimer's disease. Neurobiology of Disease (2020) Nov;145:105058. [Journal] [PDF
  • Zhang Y#, Chen Q#. Human sperm RNA code senses dietary sugar. Nature Reviews Endocrinology (2020) Apr;16(4):200-201. [Journal] [PDF]
  • Zhang X, Chen Q#. A twist between ROS and sperm-mediated intergenerational epigenetic inheritance. Molecular Cell (2020) May 7;78(3):371-373.3 [Journal] [PDF]
  • Zhang Y*, Shi J*, Rassoulzadegan M, Tuorto F, Chen Q#. Sperm RNA code programmes the metabolic health of offspring. Nature Reviews Endocrinology  (2019) Aug;15(8):489-498. [Journal] [PDF]
  • Zhang Y, Chen Q#. The expanding repertoire of hereditary information carriers. Development  (2019) Mar 15;146(6):dev170902. doi: 10.1242/dev.170902 [Journal] [PDF]

           (10/2015-1/2019) [Assistant Professor, University of Nevada, Reno]

  • Shi J*, Zhang Y*, Zhou T#, Chen Q#. tsRNAs: the Swiss army knife for translational regulation. Trends in Biochemical Sciences (2019) 44, 185-189. [Journal] [PDF]
  • Wang J, Wang L, Feng G, Wang Y, Li Y, Li X, Liu C, Jiao G, Huang C, Shi J, Zhou T, Chen Q, Liu Z, Li W#, Zhou Q#. Asymmetric Expression of LincGET Biases Cell Fate in Two-Cell Mouse Embryos. Cell  (2018) Dec 13;175(7):1887-1901.e18 [Journal] [PDF]
  • Liu Y, Chen Q#. 150 years of Darwin’s theory of intercellular flow of hereditary information. Nature Reviews Molecular Cell Biology  (2018) 19, 749–750 [Journal] [PDF]

  • Zhou T#, Xie X, Li M, Shi J, Zhou JJ, Knox KS, Wang T, Chen Q, Gu W#. Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. RNA. 2018; 24(11):1443-1456. [Journal] [PDF]
  • Chen Q*, Shi J*, Tao Y, Zernicka-Goetz M#. Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nature Communications (2018) 9:1819. DOI: 10.1038/s41467-018-04155-2 [Journal] [PDF]
  • Shi J#, Ko EA, Sanders KM, Chen Q#, Zhou T#. SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Genomics Proteomics & Bioinformatics  (2018) Apr;16(2):144-151 [Journal] [PDF]
  • Zhang Y*, Zhang X*, Shi J*, Tuorto F*, Li X*, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y#, Zhou Q#, Duan E#, Chen Q#. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature Cell Biology (2018) 20, 535–540. DOI: 10.1038/s41556-018-0087-2 [Journal] [PDF]
    -Highlighted in: Dad’s diet – smRNA methylation signatures in sperm pass on disease risk. Nat Rev Endocrinol. 2018 [PDF]