My Bibliography

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Chen Q, Jagannathan S, Reid DW, Zheng T, Nicchitta CV. Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells. Mol Biol Cell. 2011 Jul 15;22(14):2646-58. doi: 10.1091/mbc.E11-03-0239. Epub 2011 May 25. PubMed PMID: 21613539; PubMed Central PMCID: PMC3135488.

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Jagannathan S, Nwosu C, Nicchitta CV. Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation. Methods Mol Biol. 2011;714:301-21. doi: 10.1007/978-1-61779-005-8_19. PubMed PMID: 21431749; PubMed Central PMCID: PMC3718476.

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Lacsina JR, Marks OA, Liu X, Reid DW, Jagannathan S, Nicchitta CV. Premature translational termination products are rapidly degraded substrates for MHC class I presentation. PLoS One. 2012;7(12):e51968. doi: 10.1371/journal.pone.0051968. Epub 2012 Dec 14. PubMed PMID: 23251665; PubMed Central PMCID: PMC3522582.

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Jagannathan S, Hsu JC, Reid DW, Chen Q, Thompson WJ, Moseley AM, Nicchitta CV. Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum. J Biol Chem. 2014 Sep 12;289(37):25907-24. doi: 10.1074/jbc.M114.580688. Epub 2014 Jul 25. PubMed PMID: 25063809; PubMed Central PMCID: PMC4162190.

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Jagannathan S, Reid DW, Cox AH, Nicchitta CV. De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum. RNA. 2014 Oct;20(10):1489-98. doi: 10.1261/rna.045526.114. Epub 2014 Aug 20. PubMed PMID: 25142066; PubMed Central PMCID: PMC4174431.

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Feng Q, Snider L, Jagannathan S, Tawil R, van der Maarel SM, Tapscott SJ, Bradley RK. A feedback loop between nonsense-mediated decay and the retrogene DUX4 in facioscapulohumeral muscular dystrophy. Elife. 2015 Jan 7;4. doi: 10.7554/eLife.04996. PubMed PMID: 25564732; PubMed Central PMCID: PMC4383350.

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Jagannathan S, Bradley RK. Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Res. 2016 Dec;26(12):1639-1650. doi: 10.1101/gr.205070.116. Epub 2016 Sep 19. PubMed PMID: 27646533; PubMed Central PMCID: PMC5131816.

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Jagannathan S, Shadle SC, Resnick R, Snider L, Tawil RN, van der Maarel SM, Bradley RK, Tapscott SJ. Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells. Hum Mol Genet. 2016 Oct 15;25(20):4419-4431. doi: 10.1093/hmg/ddw271. PubMed PMID: 28171552; PubMed Central PMCID: PMC6078597.

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Shadle SC, Zhong JW, Campbell AE, Conerly ML, Jagannathan S, Wong CJ, Morello TD, van der Maarel SM, Tapscott SJ. DUX4-induced dsRNA and MYC mRNA stabilization activate apoptotic pathways in human cell models of facioscapulohumeral dystrophy. PLoS Genet. 2017 Mar;13(3):e1006658. doi: 10.1371/journal.pgen.1006658. eCollection 2017 Mar. PubMed PMID: 28273136; PubMed Central PMCID: PMC5362247.

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Jagannathan S, Bradley RK. Congenital myotonic dystrophy-an RNA-mediated disease across a developmental continuum. Genes Dev. 2017 Jun 1;31(11):1067-1068. doi: 10.1101/gad.302893.117. PubMed PMID: 28717044; PubMed Central PMCID: PMC5538429.

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Feng Q, Jagannathan S, Bradley RK. The RNA Surveillance Factor UPF1 Represses Myogenesis via Its E3 Ubiquitin Ligase Activity. Mol Cell. 2017 Jul 20;67(2):239-251.e6. doi: 10.1016/j.molcel.2017.05.034. Epub 2017 Jun 29. PubMed PMID: 28669802; PubMed Central PMCID: PMC5536975.

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Campbell AE, Shadle SC, Jagannathan S, Lim JW, Resnick R, Tawil R, van der Maarel SM, Tapscott SJ. NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins. Elife. 2018 Mar 13;7. doi: 10.7554/eLife.31023. PubMed PMID: 29533181; PubMed Central PMCID: PMC5849414.

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Jagannathan S, Ogata Y, Gafken PR, Tapscott SJ, Bradley RK. Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of facioscapulohumeral muscular dystrophy. Elife. 2019 Jan 15;8. doi: 10.7554/eLife.41740. PubMed PMID: 30644821; PubMed Central PMCID: PMC6349399.

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Dyle MC, Kolakada D, Cortazar MA, Jagannathan S. How to get away with nonsense: Mechanisms and consequences of escape from nonsense-mediated RNA decay. Wiley Interdiscip Rev RNA. 2020 Jan;11(1):e1560. doi: 10.1002/wrna.1560. Epub 2019 Jul 29. Review. PubMed PMID: 31359616; PubMed Central PMCID: PMC10685860.

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Jagannathan S, Ramachandran S, Rissland OS. Slow Down to Catch Up. Cell. 2019 Aug 8;178(4):774-776. doi: 10.1016/j.cell.2019.07.025. PubMed PMID: 31398334.

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Campbell AE, Dyle MC, Calviello L, Matheny T, Cortázar MA, Forman T, Fu R, Gillen AE, Floor SN, Jagannathan S. The myopathic transcription factor DUX4 induces the production of truncated RNA-binding proteins in human muscle cells. [preprint]. 2021 June. Available from: https://www.biorxiv.org/content/10.1101/2021.06.28.450189v1. doi: https://doi.org/10.1101/2021.06.28.450189.

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Child JR, Chen Q, Reid DW, Jagannathan S, Nicchitta CV. Recruitment of endoplasmic reticulum-targeted and cytosolic mRNAs into membrane-associated stress granules. RNA. 2021 Oct;27(10):1241-1256. doi: 10.1261/rna.078858.121. Epub 2021 Jul 8. PubMed PMID: 34244458; PubMed Central PMCID: PMC8456999.

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Jagannathan S, de Greef JC, Hayward LJ, Yokomori K, Gabellini D, Mul K, Sacconi S, Arjomand J, Kinoshita J, Harper SQ. Meeting report: the 2021 FSHD International Research Congress. Skelet Muscle. 2022 Jan 17;12(1):1. doi: 10.1186/s13395-022-00287-8. Review. PubMed PMID: 35039091; PubMed Central PMCID: PMC8762812.

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Jagannathan S. The evolution of DUX4 gene regulation and its implication for facioscapulohumeral muscular dystrophy. Biochim Biophys Acta Mol Basis Dis. 2022 May 1;1868(5):166367. doi: 10.1016/j.bbadis.2022.166367. Epub 2022 Feb 11. Review. PubMed PMID: 35158020; PubMed Central PMCID: PMC9173005.

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Sherlock ME, Baquero Galvis L, Vicens Q, Kieft JS, Jagannathan S. Principles, mechanisms, and biological implications of translation termination-reinitiation. RNA. 2023 Jul;29(7):865-884. doi: 10.1261/rna.079375.122. Epub 2023 Apr 6. PubMed PMID: 37024263; PubMed Central PMCID: PMC10275272.

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Campbell AE, Dyle MC, Albanese R, Matheny T, Sudheendran K, Cortázar MA, Forman T, Fu R, Gillen AE, Caruthers MH, Floor SN, Calviello L, Jagannathan S. Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression. Cell Rep. 2023 Jun 27;42(6):112642. doi: 10.1016/j.celrep.2023.112642. Epub 2023 Jun 13. PubMed PMID: 37314931; PubMed Central PMCID: PMC10592454.

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Muñoz O, Lore M, Jagannathan S. The long and short of EJC-independent nonsense-mediated RNA decay. Biochem Soc Trans. 2023 Jun 28;51(3):1121-1129. doi: 10.1042/BST20221131. Review. PubMed PMID: 37145092; PubMed Central PMCID: PMC12135299.

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Hamm DC, Paatela EM, Bennett SR, Wong CJ, Campbell AE, Wladyka CL, Smith AA, Jagannathan S, Hsieh AC, Tapscott SJ. The transcription factor DUX4 orchestrates translational reprogramming by broadly suppressing translation efficiency and promoting expression of DUX4-induced mRNAs. PLoS Biol. 2023 Sep;21(9):e3002317. doi: 10.1371/journal.pbio.3002317. eCollection 2023 Sep. PubMed PMID: 37747887; PubMed Central PMCID: PMC10553841.

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Campbell AE, Arjomand J, King OD, Tawil R, Jagannathan S. A Targeted Approach for Evaluating DUX4-Regulated Proteins as Potential Serum Biomarkers for Facioscapulohumeral Muscular Dystrophy Using Immunoassay Proteomics. J Neuromuscul Dis. 2023;10(6):1031-1040. doi: 10.3233/JND-221636. PubMed PMID: 37899061; PubMed Central PMCID: PMC10657687.

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Kolakada D, Campbell AE, Galvis LB, Li Z, Lore M, Jagannathan S. A system of reporters for comparative investigation of EJC-independent and EJC-enhanced nonsense-mediated mRNA decay. Nucleic Acids Res. 2024 Apr 12;52(6):e34. doi: 10.1093/nar/gkae121. PubMed PMID: 38375914; PubMed Central PMCID: PMC11014337.

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Calhoun JD, Dawood M, Rowlands CF, Fayer S, Radford EJ, McEwen AE, Turnbull C, Spurdle AB, Starita LM, Jagannathan S. Combining multiplexed functional data to improve variant classification. ArXiv. 2025 Mar 24;. PubMed PMID: 40196145; PubMed Central PMCID: PMC11975307.

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Kolakada D, Fu R, Biziaev N, Shuvalov A, Lore M, Campbell AE, Cortázar MA, Sajek MP, Hesselberth JR, Mukherjee N, Alkalaeva E, Coban-Akdemir ZH, Jagannathan S. Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay. Cell Genom. 2025 Jul 9;5(7):100882. doi: 10.1016/j.xgen.2025.100882. Epub 2025 May 19. PubMed PMID: 40393459; PubMed Central PMCID: PMC12278647.

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McEntee KE, McCurdy BL, Larson A, McCourt EA, Kaufman ML, Campbell AE, Pearson CG, Demarest S, Taliaferro JM, Hesselberth JR, Jagannathan S. Splice-switching antisense oligonucleotides correct cryptic exon inclusion and restore SDCCAG8 protein in Bardet-Biedl Syndrome. bioRxiv. 2025 Oct 15;. doi: 10.1101/2025.10.15.682674. PubMed PMID: 41279107; PubMed Central PMCID: PMC12632990.

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Cortázar MA, Schmidt J, Egab I, Coban-Akdemir Z, Jagannathan S. Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay. bioRxiv. 2025 Dec 23;. doi: 10.64898/2025.12.20.695734. PubMed PMID: 41509423; PubMed Central PMCID: PMC12776119.

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Cortázar MA, Jagannathan S. SelectRepair Knockout: Efficient PTC-Free Gene Knockout Through Selectable Homology-Directed DNA Repair. Methods Mol Biol. 2025;2863:397-417. doi: 10.1007/978-1-0716-4176-7_23. PubMed PMID: 39535722; PubMed Central PMCID: PMC12184210.