Publications

  • Lin Lin, Jingrong Zhao, Naoto Kubota, Zhelin Li, Yi-Li Lam, Lauren P. Nguyen, Lu Yang, Sheela P. Pokharel, Steven M. Blue, Brian A. Yee, Renee Chen, Gene W. Yeo, Chun-Wei Chen, Liang Chen, Zheng S

    • Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size
    Neuron 2024 Apr 22:S0896-6273(24)00244-7. doi: 10.1016/j.neuron.2024.04.006. (PMID: 38697111)

  • Nikom D, Zheng S

    • Alternative splicing in neurodegenerative disease and the promise of RNA therapies
    Nature Reviews Neuroscience 2023 June 19. doi: 10.1038/s41583-023-00717-6. (PMID: 3733698)

  • Hoang T, Kim DW, Appel H, Ozawa M, Zheng S, Kim J, Blackshaw S

    • Ptbp1 deletion does not induce astrocyte-to-neuron conversion.
    Nature 2023 Jun;618(7964):E1-E7.doi: 10.1038/s41586-023-06066-9. (PMID: 37286658)

  • Zhao J, Zheng S

    • Global Assessment of Protein Translation in Mammalian Cells Using Polysome Fractionation.
    Methods Mol Biol. 2023;2666:157-164. doi: 10.1007/978-1-0716-3191-1_12. (PMID: 37166664)

  • 33. Hoang T, Kim DW, Appel H, Pannullo NA, Leavey P, Ozawa M, Zheng S, Yu M, Peachey NS, Blackshaw S

    • Genetic loss of function of Ptbp1 does not induce glia-to-neuron conversion in retina.
    Cell Reports 2022 Jun 14;39(11):110849. doi: 10.1016/j.celrep.2022.110849. (PMID: 35705053)

  • Hoang T, Kim DW, Appel H, Ozawa M, Zheng S, Kim J, Blackshaw S.

    • Ptbp1 deletion does not induce astrocyte-to-neuron conversion.
    Nature 2023 Jun;618(7964):E1-E7.doi: 10.1038/s41586-023-06066-9. (PMID: 37286658)

  • Li Z, Zheng S

    • Quantitative Measurement of Alternatively Spliced RNA Isoform Levels.
    Methods Molecular Biology 2022;2537:63-79. doi: 10.1007/978-1-0716-2521-7_5.

  • Vuong JK, Ergin V, Chen L, Zheng S

    • Multilayered Regulations of Alternative Splicing, NMD, and Protein Stability Control Temporal Induction and Tissue-specific Expression of TRIM46 during Axon Formation
    Nature Communications 2022 Apr 19;13(1):2081. doi: 10.1038/s41467-022-29786-4. (PMID: 35440129)

  • Zhao J, Li Z, Puri R, Liu K, Nunez I, Chen L, Zheng S

    • Molecular profiling of individual FDA-approved clinical drugs identifies modulators of nonsense-mediated mRNA decay
    Mol Ther Nucleic Acids 2021 Dec 10;27:304-318. doi: 10.1016/j.omtn.2021.12.003. 2022 Mar 8. (PMID:35024243)

  • Jiang W, Chen L, Zheng S

    • Global reprogramming of apoptosis-related genes during brain development.
    Cells 2021 Oct 27;10(11):2901. doi: 10.3390/cells10112901 (PMID: 34831124)

  • Chen L, Zheng S

    • Understand variability of COVID-19 through population and tissue variations in expression of SARS-CoV-2 host genes.
    Inform Med Unlocked 2020;21:100443. doi: 10.1016/j.imu.2020.100443. (PMID: 33072849)
    This study show variations in COVID-19 susceptibility and symptom severity may be linked to variation in SARS-CoV-2 host gene expression.

  • Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K

    • A protein assembly mediates Xist localization and gene silencing
    Nature 2020 Nov;587(7832):145-151. doi: 10.1038/s41586-020-2703-0. (PMID: 32908311)

  • Lin L, Zhang M, Stoilov P, Chen L, Zheng S

    • Developmental attenuation of neuronal apoptosis by neural specific splicing of Bak1 microexon
    Neuron 2020 Sep 23;107(6):1180-1196.e8. doi: 10.1016/j.neuron.2020.06.036. (PMID: 32710818)
    In contrast to the dogma that neuronal survival is enabled by target tissues, this study shows apoptotic resistance is not a “toggle switch” imposed by fruitful neuronal connections but rather starts as early as neuron birth through neural-specific splicing of Bak1 exon 5. It also shows attenuation of apoptosis competence is essential for neuronal and animal survival.

  • Ergin V, Zheng S

    • Putative coiled-coil domain dependent autoinhibition and alternative splicing determine SHTN1’s actin activity
    Journal of Molecular Biology 2020 (PMID: 32371045)
    This study shows SHTN1 has a noncanonical actin-binding domain, which is auto-inhibited unconventionally by a N-terminal coiled-coil domain. Unlike any autoinhibited actin-binding proteins, which employ a third protein to turn on actin binding, SHTN1 uses alternative splicing of its C-terminal to relieve autoinhibition.

  • Zheng S

    • Alternative splicing programming of axon formation
    Wiley Interdiscip Rev RNA 2020 Jan 10:e1585. doi: 10.1002/wrna.1585. (PMID: 31922356).
    This review uniquely distinguishes multiple aspects of axonogenesis and comprehensively explain the contribution of alternative splicing regulation to each aspect.

  • Soto EL, Gandal M, Gonatopoulos-Pournatzis T, Heller E, Luo D, Zheng S.

    • Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions
    Journal of Neuroscience 2019 Oct 16; 39(42): 8193-8199. (PMID: 31619487).

  • Zhang M, Ergin V, Lin L, Stork C, Chen L, Zheng S.

    • Axonogenesis is coordinated by alternative splicing programming and splicing regulator PTBP2
    Neuron 2019 Feb 20; 101(4): 690-706. (PMID: 30733148).

  • Stork C, Li Z, Lin L, Zheng S.

    • Developmental Xist induction is mediated by enhanced splicing.
    Nucleic Acids Res. 2019 Feb 20; 47(3): 1532-1453. (PMID: 30496473).

  • Chen L, Zheng S.

    • BCseq: accurate single cell RNA-seq quantification with bias correction.
    Nucleic Acids Res. 2018 Aug 21;46(14):e82 (PMID: 29718338).

  • Stork C, Zheng S.

    • High-throughput screening method to identify alternative splicing regulators.
    Methods Mol Biol. 2018;1755:65-74 (PMID: 29671263).

  • Zheng S.

    • Cell-Based High-Throughput Method for Identifying Modulators of Alternative Splicing.
    Methods Mol Biol. 2017;1648:221-233.

  • Li Z, Vuong JK, Zhang M, Stork C, Zheng S.

    • Inhibition of nonsense-mediated RNA decay by ER stress.
    RNA 2017 Mar;23(3):378-394 (PMID: 27940503).

  • Vuong JK, Lin CH, Zhang M, Chen L, Black DL, Zheng S.

    • PTBP1 and PTBP2 serve both specific and redundant functions in neuronal pre-mRNA splicing.
    Cell Reports 2016 Dec 6;17(10):2766-2775.

  • Zheng S.

    • IRAS: High-Throughput Identification of Novel Alternative Splicing Regulators.
    Methods in Enzymology 2016;572:269-89.

  • Vuong CK, Black DL, Zheng S.

    • The neurogenetics of alternative splicing.
    Nature Reviews Neuroscience 2016 Apr 20;17(5):265-81.

  • Zheng S.

    • Alternative splicing and nonsense-mediated mRNA decay enforce neural specific gene expression.
    International Journal of Developmental Neuroscience 2016 Mar 8. pii: S0736-5748(16)30005-3.

  • Stork C, Zheng S.

    • Genome-wide profiling of RNA-protein interactions using CLIP-Seq.
    Methods in Molecular Biology 2016;1421:137-51.

  • Li Q, Zheng S, Han A, Lin C, Stoilov P, Fu XD, Black DL.

    • The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation.
    eLife 2014 Jan 21; 3(0): e01201 (PMC3896118).

  • Zheng S, Black DL.

    • Alternative pre-mRNA splicing in neurons: growing up and extending its reach.
    Trends Genet 2013 Aug;29(8):442-8.

  • Zheng S, Damoiseaux R, Chen L, Black DL.

    • A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing.
    Genome Research 2013 23(6): p. 998-1007.

  • Zheng S, Gray EE, Chawla G, Porse BT, O'Dell TJ, Black DL.

    • PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2.
    Nat Neurosci 2012 Jan 15;15(3):381-8 (PMC3288398).

  • Tang ZZ, Sharma S, Zheng S, Chawla G, Nikolic J, Black DL.

    • Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein.
    J Biol Chem 2011 Mar 25;286(12):10007-16.

  • Zheng S, Eacker SM, Hong SJ, Gronostajski RM, Dawson TM, Dawson VL.

    • NMDA-induced neuronal survival is mediated through nuclear factor I-A in mice.
    J Clin Invest 2010 Jul;120(7):2446-56.

  • Tang ZZ, Zheng S, Nikolic J, Black DL.

    • Developmental control of CaV1.2 L-type calcium channel splicing by Fox proteins.
    Mol Cell Biol 2009 Sep;29(17):4757-65.

  • Zheng S, Chen L.

    • A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level.
    Nucleic Acids Res 2009 Jun;37(10):e75.

  • Chen L, Zheng S.

    • Studying alternative splicing regulatory networks through partial correlation analysis.
    Genome Biol 2009;10(1):R3.

  • Chen L, Zheng S.

    • Identify alternative splicing events based on position-specific evolutionary conservation.
    PLoS One 2008 Jul 30;3(7):e2806.

    © 2014 The Zheng laboratory