Publications

Barr K, He KL, Krumbein AJ, Chanfreau GF. Transcription termination promotes splicing efficiency and fidelity in a compact genome. bioRxiv [Preprint]. 2025 Mar 12:2025.03.12.642901. doi: 10.1101/2025.03.12.642901. PMID: 40161703; PMCID: PMC11952531.

He K, Chanfreau GF. Detection of Nuclear RNA Decay Intermediates Using a Modified Oxford Nanopore RNA Sequencing Strategy. Methods Mol Biol. 2025;2863:339-358. doi: 10.1007/978-1-0716-4176-7_20. PMID: 39535719.

Novales NA, Feustel KJ, He KL, Chanfreau GF, Clarke CF. Nonfunctional coq10 mutants maintain the ERMES complex and reveal true phenotypes associated with the loss of the coenzyme Q chaperone protein Coq10. J Biol Chem. 2024 Nov;300(11):107820. doi: 10.1016/j.jbc.2024.107820. Epub 2024 Sep 27. PMID: 39343004; PMCID: PMC11541779.

Higginson LA, Wang X, He K, Torstrick M, Kim M, Benayoun BA, MacLean A, Chanfreau GF, Morton DJ. The RNA exosome maintains cellular RNA homeostasis by controlling transcript abundance in the brain. bioRxiv [Preprint]. 2024 Oct 30:2024.10.30.620488. doi: 10.1101/2024.10.30.620488. PMID: 39554067; PMCID: PMC11565928.

Krieger MR, Abrahamian M, He KL, Atamdede S, Hakimjavadi H, Momcilovic M, Ostrow D, Maggo SD, Tsang YP, Gai X, Chanfreau GF, Shackelford DB, Teitell MA, Koehler CM. Trafficking of mitochondrial double-stranded RNA from mitochondria to the cytosol. Life Sci Alliance. 2024 Jul 2;7(9):e202302396. doi: 10.26508/lsa.202302396. PMID: 38955468; PMCID: PMC11220484.

Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau GF, Hoskins AA. Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7. RNA. 2024 Jul 16;30(8):1058-1069. doi: 10.1261/rna.079956.124. PMID: 38719745; PMCID: PMC11251517.

Bremer KV, Wu C, Patel AA, He KL, Grunfeld AM, Chanfreau GF, Quinlan ME. Formin tails act as a switch, inhibiting or enhancing processive actin elongation. J Biol Chem. 2024 Jan;300(1):105557. doi: 10.1016/j.jbc.2023.105557. Epub 2023 Dec 12. PMID: 38097186; PMCID: PMC10797183.

Roy KR, Gabunilas J, Neutel D, Ai M, Yeh Z, Samson J, Lyu G, Chanfreau GF. Splicing factor Prp18p promotes genome-wide fidelity of consensus 3'-splice sites. Nucleic Acids Res. 2023 Dec 11;51(22):12428-12442. doi: 10.1093/nar/gkad968. PMID: 37956322; PMCID: PMC10711555.

DeMario S, Xu K, He K, Chanfreau GF. Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data. RNA. 2023 Aug;29(8):1099-1107. doi: 10.1261/rna.079505.122. Epub 2023 May 3. PMID: 37137666; PMCID: PMC10351882.

Roy KR, Gabunilas J, Neutel D, Ai M, Samson J, Lyu G, Chanfreau GF. Spliceosomal mutations decouple 3' splice site fidelity from cellular fitness. bioRxiv [Preprint]. 2023 Jan 12:2023.01.12.523824. doi: 10.1101/2023.01.12.523824. PMID: 36711521; PMCID: PMC9882110.

Liu Y, DeMario S, He K, Gibbs MR, Barr KW, Chanfreau GF. Splicing inactivation generates hybrid mRNA-snoRNA transcripts targeted by cytoplasmic RNA decay. Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2202473119. doi: 10.1073/pnas.2202473119. Epub 2022 Jul 25. PMID: 35878033; PMCID: PMC9351541.

Gibbs MR, Chanfreau GF. UPF1 adds an m6A feather to its (de)cap. Cell Rep. 2022 May 24;39(8):110898. doi: 10.1016/j.celrep.2022.110898. PMID: 35613576.

Wang C, Barr K, Neutel D, Roy K, Liu Y, Chanfreau GF. Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the  BDF2 mRNA. RNA. 2021 Dec;27(12):1545-1556. doi: 10.1261/rna.078880.121. Epub 2021 Sep 8. PMID: 34497070; PMCID: PMC8594472.

Weathers I, Gabunilas J, Samson J, Roy K, Chanfreau GF. Protocol for High- Resolution Mapping of Splicing Products and Isoforms by RT-PCR Using Fluorescently Labeled Primers. STAR Protoc. 2020 Oct 21;1(3):100140. doi: 10.1016/j.xpro.2020.100140. PMID: 33377034; PMCID: PMC7757285.

Wang C, Liu Y, DeMario SM, Mandric I, Gonzalez-Figueroa C, Chanfreau GF. Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress. Cell Rep. 2020 Jun 9;31(10):107754. doi: 10.1016/j.celrep.2020.107754. PMID: 32521279; PMCID: PMC7587046.

Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. Methods. 2020 Apr 1;176:4-13. doi: 10.1016/j.ymeth.2019.05.016. Epub 2019 May 23. PMID: 31128237; PMCID: PMC6874744.

White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry. 2019 Dec 10;58(49):4997-5010. doi: 10.1021/acs.biochem.9b00818. Epub 2019 Dec 2. PMID: 31738538; PMCID: PMC6913935.

Roy K, Chanfreau GF. A global function for transcription factors in assisting RNA polymerase II termination. Transcription. 2018;9(1):41-46. doi: 10.1080/21541264.2017.1300121. Epub 2017 Nov 6. PMID: 29106321; PMCID: PMC5791854.

Gillespie A, Gabunilas J, Jen JC, Chanfreau GF. Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae. RNA. 2017 Apr;23(4):466-472. doi: 10.1261/rna.060004.116. Epub 2017 Jan 4. PMID: 28053271; PMCID: PMC5340910.

Chanfreau GF. Preface. Enzymes. 2017;41:xi. doi: 10.1016/S1874-6047(17)30017-3. PMID: 28601228.

Chanfreau GF. Impact of RNA Modifications and RNA-Modifying Enzymes on Eukaryotic Ribonucleases. Enzymes. 2017;41:299-329. doi: 10.1016/bs.enz.2017.03.008. Epub 2017 May 5. PMID: 28601225.

Roy K, Gabunilas J, Gillespie A, Ngo D, Chanfreau GF. Common genomic elements promote transcriptional and DNA replication roadblocks. Genome Res. 2016 Oct;26(10):1363-1375. doi: 10.1101/gr.204776.116. Epub 2016 Aug 18. PMID: 27540088; PMCID: PMC5052057.

Kaweeteerawat C, Chang CH, Roy KR, Liu R, Li R, Toso D, Fischer H, Ivask A, Ji Z, Zink JI, Zhou ZH, Chanfreau GF, Telesca D, Cohen Y, Holden PA, Nel AE, Godwin HA. Cu Nanoparticles Have Different Impacts in Escherichia coli and Lactobacillus brevis than Their Microsized and Ionic Analogues. ACS Nano. 2015 Jul 28;9(7):7215-25. doi: 10.1021/acsnano.5b02021. Epub 2015 Jul 13. PMID: 26168153; PMCID: PMC5698005.

Dzialo MC, Travaglini KJ, Shen S, Roy K, Chanfreau GF, Loo JA, Clarke SG. Translational roles of elongation factor 2 protein lysine methylation. J Biol Chem. 2014 Oct 31;289(44):30511-30524. doi: 10.1074 jbc.M114.605527. Epub 2014 Sep 17. PMID: 25231983; PMCID: PMC4215232.

Al-Hadid Q, Roy K, Munroe W, Dzialo MC, Chanfreau GF, Clarke SG. Histidine methylation of yeast ribosomal protein Rpl3p is required for proper 60S subunit assembly. Mol Cell Biol. 2014 Aug;34(15):2903-16. doi: 10.1128/MCB.01634-13. Epub 2014 May 27. PMID: 24865971; PMCID: PMC4135575.

Kawashima T, Douglass S, Gabunilas J, Pellegrini M, Chanfreau GF. Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae. PLoS Genet. 2014 Apr 10;10(4):e1004249. doi: 10.1371/journal.pgen.1004249. PMID: 24722551; PMCID: PMC3983031.

Chanfreau GF. Zinc’ing down RNA polymerase I. Transcription. 2013 Sep-Dec;4(5):217-20. doi: 10.4161/trns.26594. PMID: 24135703; PMCID: PMC4114658.

Lee YJ, Lee CY, Grzechnik A, Gonzales-Zubiate F, Vashisht AA, Lee A, Wohlschlegel J, Chanfreau GF. RNA polymerase I stability couples cellular growth to metal availability. Mol Cell. 2013 Jul 11;51(1):105-15. doi: 10.1016/j.molcel.2013.05.005. Epub 2013 Jun 6. PMID: 23747013; PMCID: PMC3713077.

Sayani S, Chanfreau GF. Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae. RNA. 2012 Aug;18(8):1563-72. doi: 10.1261/rna.033779.112. Epub 2012 Jul 2. PMID: 22753783; PMCID: PMC3404376.

Egecioglu DE, Kawashima TR, Chanfreau GF. Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation. Nucleic Acids Res. 2012 Feb;40(4):1787-96. doi: 10.1093/nar/gkr864. Epub 2011 Oct 22. PMID: 22021379; PMCID: PMC3287188.

Roy K, Chanfreau GF. The Diverse Functions of Fungal RNase III Enzymes in RNA Metabolism. Enzymes. 2012;31:213-35. doi: 10.1016/B978-0-12-404740-2.00010-0. Epub 2012 Sep 29. PMID: 27166447.

Toesca I, Nery CR, Fernandez CF, Sayani S, Chanfreau GF. Cryptic transcription mediates repression of subtelomeric metal homeostasis genes. PLoS Genet. 2011 Jun;7(6):e1002163. doi: 10.1371/journal.pgen.1002163. Epub 2011 Jun 30. PMID: 21738494; PMCID: PMC3128112.

Chanfreau GF. A dual role for RNA splicing signals. EMBO Rep. 2010 Oct;11(10):720-1. doi: 10.1038/embor.2010.148. PMID: 20877291; PMCID: PMC2948198.

Kawashima T, Pellegrini M, Chanfreau GF. Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations. RNA. 2009 Dec;15(12):2236-47. doi: 10.1261/rna.1736809. Epub 2009 Oct 22. PMID: 19850912; PMCID: PMC2779665.

Sayani S, Janis M, Lee CY, Toesca I, Chanfreau GF. Widespread impact of nonsense-mediated mRNA decay on the yeast intronome. Mol Cell. 2008 Aug 8;31(3):360-70. doi: 10.1016/j.molcel.2008.07.005. PMID: 18691968; PMCID: PMC2600495.

Egecioglu DE, Henras AK, Chanfreau GF. Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA. 2006 Jan;12(1):26-32. doi: 10.1261/rna.2207206. PMID: 16373491; PMCID: PMC1370882.

Chanfreau GF. CUTting genetic noise by polyadenylation-induced RNA degradation. Trends Cell Biol. 2005 Dec;15(12):635-7. doi: 10.1016/j.tcb.2005.10.004. Epub 2005 Oct 21. PMID: 16243527.

Henras AK, Sam M, Hiley SL, Wu H, Hughes TR, Feigon J, Chanfreau GF. Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III. RNA. 2005 Aug;11(8):1225-37. doi: 10.1261/rna.2760705. Epub 2005 Jun 29. PMID: 15987808; PMCID: PMC1370806.