Publications | DFU Lab

https://www.ncbi.nlm.nih.gov/myncbi/dragony.fu.1/bibliography/public/

Zhang K, Ciesla JH, Eldin P, Briant L, Lentini JM, Ramos J, Munger J, Fu D. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease. BioRxiv [preprint]. 2023 February. bioRxiv 2023.02.10.527147Available from: https://doi.org/10.1101/2023.02.10.527147.
Hogan CA, Gratz SJ, Dumouchel JL, Thakur RS, Delgado A, Lentini JM, Madhwani KR, Fu D, O’Connor-Giles KM. Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function. EMBO Rep. 2023 Oct 9;24(10):e56808. doi: 10.15252/embr.202356808. Epub 2023 Aug 29. PubMed PMID: 37642556; PubMed Central PMCID: PMC10561368.
Longan ER, Ramos J, Fu D. ADATscan – A flexible tool for scanning exomes for wobble inosine-dependent codons reveals a neurological bias for genes enriched in such codons in humans and mice. MicroPubl Biol. 2023;2023. doi: 10.17912/micropub.biology.000675. eCollection 2023. PubMed PMID: 36733466; PubMed Central PMCID: PMC9887483.
Lentini JM, Bargabos R, Chen C, Fu D. Methyltransferase METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs. J Biol Chem. 2022 Apr;298(4):101788. doi: 10.1016/j.jbc.2022.101788. Epub 2022 Mar 3. PubMed PMID: 35247384; PubMed Central PMCID: PMC8980813.
Broly M, Polevoda BV, Awayda KM, Tong N, Lentini J, Besnard T, Deb W, O’Rourke D, Baptista J, Ellard S, Almannai M, Hashem M, Abdulwahab F, Shamseldin H, Al-Tala S, Alkuraya FS, Leon A, van Loon RLE, Ferlini A, Sanchini M, Bigoni S, Ciorba A, van Bokhoven H, Iqbal Z, Al-Maawali A, Al-Murshedi F, Ganesh A, Al-Mamari W, Lim SC, Pais LS, Brown N, Riazuddin S, Bézieau S, Fu D, Isidor B, Cogné B, O’Connell MR. THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder. Am J Hum Genet. 2022 Apr 7;109(4):587-600. doi: 10.1016/j.ajhg.2022.02.001. Epub 2022 Feb 22. PubMed PMID: 35196516; PubMed Central PMCID: PMC9069073.
Ramos J, Fu D. Detection of tRNA-specific adenosine deaminase activity and wobble inosine modification in human cell lysates. Methods Enzymol. 2021;658:311-334. doi: 10.1016/bs.mie.2021.06.008. Epub 2021 Jul 24.PMID: 34517952.
Lentini JM, Fu D. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease. Methods Mol Biol. 2021;2298:197-216. doi: 10.1007/978-1-0716-1374-0_13. PubMed PMID: 34085247.
Kulkarni CA, Nadtochiy SM, Kennedy L, Zhang J, Chhim S, Alwaseem H, Murphy E, Fu D, Brookes PS.ALKBH7 mediates necrosis via rewiring of glyoxal metabolism. Elife. 2020 Aug 14;9. doi: 10.7554/eLife.58573. PubMed PMID: 32795389; PubMed Central PMCID: PMC7442491.
Ramos J, Proven M, Halvardson J, Hagelskamp F, Kuchinskaya E, Phelan B, Bell R, Kellner S, Feuk L, Thuresson AC, Fu D. Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder. RNA. 2020 Aug 6;. doi: 10.1261/rna.076380.120. [Epub ahead of print] PubMed PMID: 32763916.
Lentini JM, Alsaif HS, Faqeih E, Alkuraya FS, Fu D. DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Nature Commun. 2020 May 19;11(1):2510. doi: 10.1038/s41467-020-16321-6. PubMed PMID: 32427860; PubMed Central PMCID: PMC7237682.
Hagelskamp F, Borland K, Ramos J, Hendrick AG, Fu D, Kellner S. Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro. Nucleic Acids Res. 2020 Apr 17;48(7):e41. doi: 10.1093/nar/gkaa091. PubMed PMID: 32083657; PubMed Central PMCID: PMC7144906.
Zhang K, Lentini JM, Prevost CT, Hashem MO, Alkuraya FS, Fu D. An intellectual disability-associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity. Hum Mutat. 2020 Jan 3;. doi: 10.1002/humu.23976. [Epub ahead of print] PubMed PMID: 31898845.
Shaheen R, Mark P, Prevost CT, AlKindi A, Alhag A, Estwani F, Al-Sheddi T, Alobeid E, Alenazi MM, Ewida N, Ibrahim N, Hashem M, Abdulwahab F, Bryant EM, Spinelli E, Millichap J, Barnett SS, Kearney HM, Accogli A, Scala M, Capra V, Nigro V, Fu D, Alkuraya FS. Biallelic variants in CTU2 cause DREAM-PL syndrome and impair thiolation of tRNA wobble U34. Hum Mutat. 2019 Jul 13;. doi: 10.1002/humu.23870. [Epub ahead of print] PubMed PMID: 31301155.
Ramos J, Han L, Li Y, Hagelskamp F, Kellner SM, Alkuraya FS, Phizicky EM, Fu D. Formation of tRNA wobble inosine in humans is disrupted by a millennia-old mutation causing intellectual disability. Mol Cell Biol. 2019 Jul 1;. doi: 10.1128/MCB.00203-19. [Epub ahead of print] PubMed PMID: 31263000.
Ramos J, Fu D. The emerging impact of tRNA modifications in the brain and nervous system. Biochim Biophys Acta Gene Regul Mech. 2019 Mar;1862(3):412-428. doi: 10.1016/j.bbagrm.2018.11.007. Epub 2018 Dec 5. Review. PubMed PMID: 30529455.
Gu C, Ramos J, Begley U, Dedon PC, Fu D, Begley TJ. Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression. Sci Adv. 2018 Jul;4(7):eaas9184. doi: 10.1126/sciadv.aas9184. eCollection 2018 Jul. PubMed PMID: 30009260; PubMed Central PMCID: PMC6040840.
Lentini JM, Ramos J, Fu D. Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the γ-toxin endonuclease. RNA. 2018 May;24(5):749-758. doi: 10.1261/rna.065581.118. Epub 2018 Feb 13. PubMed PMID: 29440318; PubMed Central PMCID: PMC5900570.
Padgett LR, Lentini JM, Holmes MJ, Stilger KL, Fu D, Sullivan WJ Jr. Elp3 and RlmN: A tale of two mitochondrial tail-anchored radical SAM enzymes in Toxoplasma gondii. PLoS One. 2018;13(1):e0189688. doi: 10.1371/journal.pone.0189688. eCollection 2018. PubMed PMID: 29293520; PubMed Central PMCID: PMC5749711.
Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Mol Cell Biol. 2017 Nov 1;37(21). doi: 10.1128/MCB.00214-17. Print 2017 Nov 1. PubMed PMID: 28784718; PubMed Central PMCID: PMC5640816.
Jordan JJ, Chhim S, Margulies CM, Allocca M, Bronson RT, Klungland A, Samson LD, Fu D. ALKBH7 drives a tissue and sex-specific necrotic cell death response following alkylation-induced damage. Cell Death Dis. 2017 Jul 20;8(7):e2947. doi: 10.1038/cddis.2017.343. PubMed PMID: 28726787; PubMed Central PMCID: PMC5550884.
Nadtochiy SM, Schafer X, Fu D, Nehrke K, Munger J, Brookes PS. Acidic pH Is a Metabolic Switch for 2-Hydroxyglutarate Generation and Signaling. J Biol Chem. 2016 Sep 16;291(38):20188-97. doi: 10.1074/jbc.M116.738799. Epub 2016 Aug 10. PubMed PMID: 27510037; PubMed Central PMCID: PMC5025701.

Postdoctoral

Fu D, Samson LD, Hübscher U, van Loon B. The interaction between ALKBH2 DNA repair enzyme and PCNA is direct, mediated by the hydrophobic pocket of PCNA and perturbed in naturally-occurring ALKBH2 variants. DNA Repair (Amst).2015 Nov;35:13-8. doi: 10.1016/j.dnarep.2015.09.008. Epub 2015 Sep 14. PubMed PMID: 26408825; PubMed Central PMCID: PMC5206904.
Fu D, Jordan JJ, Samson LD. Human ALKBH7 is required for alkylation and oxidation-induced programmed necrosis.Genes Dev. 2013 May 15;27(10):1089-100. doi: 10.1101/gad.215533.113. Epub 2013 May 10. PubMed PMID: 23666923; PubMed Central PMCID: PMC3672644.
Fu D, Calvo JA, Samson LD. Balancing repair and tolerance of DNA damage caused by alkylating agents. Nat Rev Cancer.2012 Jan 12;12(2):104-20. doi: 10.1038/nrc3185. Review. PubMed PMID: 22237395; PubMed Central PMCID: PMC3586545.
Fu D, Samson LD. Direct repair of 3,N(4)-ethenocytosine by the human ALKBH2 dioxygenase is blocked by the AAG/MPG glycosylase. DNA Repair (Amst). 2012 Jan 2;11(1):46-52. doi: 10.1016/j.dnarep.2011.10.004. Epub 2011 Nov 11. PubMed PMID: 22079122; PubMed Central PMCID: PMC3253959.
Fu D, Brophy JA, Chan CT, Atmore KA, Begley U, Paules RS, Dedon PC, Begley TJ, Samson LD. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol. 2010 May;30(10):2449-59. doi: 10.1128/MCB.01604-09. Epub 2010 Mar 22. PubMed PMID: 20308323; PubMed Central PMCID: PMC2863699.

Graduate
Errington TM, Fu D, Wong JM, Collins K. Disease-associated human telomerase RNA variants show loss of function for telomere synthesis without dominant-negative interference. Mol Cell Biol. 2008 Oct;28(20):6510-20. doi: 10.1128/MCB.00777-08. Epub 2008 Aug 18. PubMed PMID: 18710936; PubMed Central PMCID: PMC2577424.
Fu D, Collins K. Purification of human telomerase complexes identifies factors involved in telomerase biogenesis and telomere length regulation. Mol Cell. 2007 Dec 14;28(5):773-85. doi: 10.1016/j.molcel.2007.09.023. PubMed PMID: 18082603; PubMed Central PMCID: PMC2917595.
Fu D, Collins K. Human telomerase and Cajal body ribonucleoproteins share a unique specificity of Sm protein association. Genes Dev. 2006 Mar 1;20(5):531-6. doi: 10.1101/gad.1390306. Epub 2006 Feb 15. PubMed PMID: 16481465; PubMed Central PMCID: PMC1410806.
Fu D, Collins K. Distinct biogenesis pathways for human telomerase RNA and H/ACA small nucleolar RNAs. Mol Cell. 2003 May;11(5):1361-72. PubMed PMID: 12769858.

Undergraduate and Post-Baccalaureate
Xiao H, Sandaltzopoulos R, Wang HM, Hamiche A, Ranallo R, Lee KM, Fu D, Wu C. Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol Cell. 2001 Sep;8(3):531-43. PubMed PMID: 11583616.
Payne WE, Kaiser CA, Bevis BJ, Soderholm J, Fu D, Sears IB, Glick BS. Isolation of Pichia pastoris genes involved in ER-to-Golgi transport. Yeast. 2000 Aug;16(11):979-93. doi: 10.1002/1097-0061(200008)16:11<979::AID-YEA594>3.0.CO;2-C. PubMed PMID: 10923020.