Selected Publications

Original Research Articles:

Ganesan R, Mangkalaphiban K, Baker RE, He F, Jacobson A. Ribosome-bound Upf1 forms distinct 80S complexes and conducts mRNA surveillance. RNA. 2022 12; 28(12):1621-1642. PMID: 36192133.

He F, Wu C, Jacobson A. Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes. Elife. 2022 05 23; 11. PMID: 35604319.

Mangkalaphiban K, He F, Ganesan R, Wu C, Baker R, Jacobson A. Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. PLoS Genet. 2021 04; 17(4):e1009538. PMID: 33878104.

Wu, C., Roy, B., He, F., Yan, K., Jacobson, A. Poly(A)-binding protein regulates the efficiency of translation termination. Cell Reports 33: 108399, (2020). PMID: 33207198

He, F., Celik, A., and Jacobson, A. General decapping activators target different subsets of inefficiently translated mRNAs. eLife 7: e34409, (2018). PMID: 30520724

Celik, A., Baker, R., He, F., and Jacobson, A. High resolution profiling of NMD substrates in yeast reveals translational fidelity as a basis for substrate selection. RNA 23: 735-748, (2017). PMID: 28209632

He, F. and Jacobson, A. Control of mRNA decapping by positive and negative regulatory elements in the C-terminal domain of Dcp2. RNA 21:1633-1647. (2015). PMID: 26184073

Amcheslavsky, A., Nie, Y., Li, Q., He, F., Tsuda, L., Markstein, M., and Ip, Y.T. Gene expression profiling identifies the zinc-finger protein Charlatan as a regulator of intestinal stem cells in Drosophila. Development 141:2621-2632. (2014). PMID: 24961799

He, F., Li, C., Roy, B., and Jacobson, A. Yeast Edc3 targets RPS28B mRNA for decapping by binding to a 3’-UTR decay-inducing regulatory element. Mol. Cell. Biol. 34:1438-1451. (2014). PMID: 24492965

He F, Ganesan R, Jacobson A. Intra- and intermolecular regulatory interactions in Upf1, the RNA helicase central to nonsense-mediated mRNA decay in yeast. Mol Cell Biol. 2013 Dec; 33(23):4672-84. PMID: 24100012.

Min, E., Roy, B., Amrani, N., He, F., and Jacobson, A. Yeast Upf1 CH domain interacts with Rps26 of the 40S ribosomal subunit. RNA 19: 1105-1115. (2013). PMID: 23801788

Landrette, S. F., Madera, D., He, F., and Castilla, L. H. The transcription factor PlagL2 activates Mpl transcription and signaling in hematopoietic progenitor and leukemia cells. Leukemia 25:655-662. (2011). PMID: 21263445

Dong, S., Jacobson, A., and He, F. Edc3p-mediated cytoplasmic YRA1 pre-mRNA degradation requires multiple intronic modular elements, translational repression, and Mex67p. PLoS Biology 8: e1000360. (2010). PMID: 20463951

ohansson, M. J.O., He, F., Spatrick, P., Li, C., and Jacobson, A. Association of yeast Upf1p with direct substrates of the NMD pathway. Proc. Natl. Acad. Sci. USA 104:20872-20877. (2007). PMID: 18087042

Dong, S., Li, C., Zenklusen, D., Singer, R.H., Jacobson, A., and He, F. YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol. Cell 25:559-573. (2007). PMID: 17317628

Welch, E.M., Barton, E.R.et al. PTC124 targets genetic disorders caused by nonsense mutations. Nature 447:87-91. (2007). PMID: 17450125

Wang, S., Farfan-Arribas, D. J., Shen, S., Chou, T.-h. W., Hirsch, A., He, F., and Lu, S. Relative contributions of codon usage, promoter efficiency and leader sequence to the antigen expression and immunogenicity of HIV-1 Env DNA vaccine. Vaccine 24, 4531-4540. (2006). PMID: 16140431

Parker, K.C., Patterson, D., Williamson, B., Marchese, J., Graber, A., He, F., Jacobson, A., Juhasz, P., and Martin, S. Depth of proteome issues: a yeast isotope-coded affinity tag reagent study. Mol. Cell. Proteomics 3:625-659. (2004). PMID: 15047794

Ross, P.L., Huang, Y.N., Marchese, J.N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Daniels, S., Purkayastha, S., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3:1154-1169. (2004). PMID: 15385600.

Li, L., He, F., Litofsky, N. S., Recht, L. D., and Ross, A.H. Profiling of genes expressed by PTEN haploinsufficient neural precursor cells. Mol. and Cell. Neuroscience 24:1051-1061. (2003). PMID: 14697668

Maderazo, A.B., Belk, J.P., He, F., and Jacobson, A. Nonsense-containing mRNAs that accumulate in the absence of a functional NMD pathway are destabilized rapidly upon its restitution. Mol. Cell. Biol. 23:842-851. (2003). PMID: 12529390

He, F., Li, X., Spatrick, P., Casillo, R., Dong, S., and Jacobson, A. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol. Cell 12:1439-1452. (2003). PMID: 14690598

Liu, H., Radhakrishnan, P., Magoun, L., Prabu, M., Campellone, K.G., Savage, P., He, F., Schiffer, C.A., and. Leong, J.M. Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket. Mol. Microbiol. 45:1557-1573. (2002). PMID: 12354225

Bond, A. T., Mangus, D. A., He, F., and Jacobson, A. Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing. Mol. Cell. Biol. 21:7366-7379. (2001). PMID: 11585918

He, F. and Jacobson, A. Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs. Mol. Cell. Biol. 21:1515-1530. (2001). PMID: 11238889

Bhattacharya, A., Czaplinski, K., Trifillis, P., He, F., Jacobson, A., and Peltz, S.W. Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. RNA 6:1226-1235. (2000). PMID: 10999600

Maderazo, A.B., He, F., Mangus, D.A., and Jacobson, A. Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p. Mol. Cell. Biol. 20:4591-4603. (2000). PMID: 10848586

Belk, J. P., He, F., and Jacobson, A. Overexpression of truncated Nmd3p inhibits protein synthesis in yeast. RNA 5:1055-1070. (1999). PMID: 10445880 He, F., Brown, A.H., and Jacobson, A. Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway. Mol. Cell. Biol. 17:1580-1594. (1997). PMID: 9032286

He, F., Brown, A. H., and Jacobson, A. Interaction between Nmd2p and Upf1p is required for activity but not for dominant-negative inhibition of the nonsense-mediated mRNA decay pathway in yeast. RNA 2:153-170. (1996). PMID: 8601282

He, F. and Jacobson, A. Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen. Genes & Devel. 9:437-454. (1995). PMID: 7883168 He, F., Peltz, S.W., Donahue, J.L., Rosbash, M., and Jacobson, A. Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant. Proc. Natl. Acad. Sci. USA 90:7034-7038. (1993). PMID: 8346213

Fournier, P., Abbas, A., Chasles, M., Kudla, B., Ogrydziak, D., Yaver, D., Xuan, J., Peito, A., Ribet, A., Feynerol, C., He, F., and Gaillardin, C. Colocalization of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica. Proc. Natl. Acad. Sci. USA 90:4912-4916. (1993). PMID: 8506336

He, F., Beckerich, J.M., and Gaillardin, C. A mutant of 7SL RNA in Yarrowia lipolytica affecting the synthesis of a secreted protein. J. Biol. Chem. 267:1932-1937. (1992). PMID: 1309803

He, F., Yaver, D., Beckerich, J. M., Ogrydziak, D., and Gaillardin, C. The yeast Yarrowia lipolytica has two, functional, signal recognition particle 7S RNA genes. Curr. Genet. 17:289-292. (1990). PMID: 2160331

He, F., Beckerich, J.M., Ribes, V., Tollervey, D., and. Gaillardin. C. Two genes encode 7SL RNAs in the yeast Yarrowia lipolytica. Curr. Genet. 16:347-350. (1989). PMID: 2558808

Review articles:

He F, Jacobson A. Eukaryotic mRNA decapping factors: molecular mechanisms and activity. FEBS J. 2023 11; 290(21):5057-5085. PMID: 36098474.

Celik, A., He, F., and Jacobson, A. NMD monitors translational fidelity 24/7. Current Genet. 63: 1007-1010, (2017). PMID: 28536849

He, F. and Jacobson, A. Nonsense-mediated mRNA decay: degradation of defective transcripts is only part of the story. Ann. Rev. Genet. 49:339-66. (2015). PMID: 26436458

Amrani, N., Dong, S., He, F., Ganesan, R., Ghosh, S., Kervestin, S., Li, C., Mangus, D.A., Spatrick, P., and Jacobson, A. Aberrant termination triggers nonsense-mediated mRNA decay. Biochem. Soc. Transact. 34:39-42. (2006). PMID: 16246174

Peltz, S. W., He, F., Welch, E., and A. Jacobson. Nonsense-mediated mRNA decay in yeast. Prog. Nucleic. Acid Res. Mol. Biol. 47:271-298. (1994). PMID: 8016322

Book chapters:

He, F., Celik, A., Baker, R., and Jacobson, A. High resolution profiling of NMD targets in yeast. In: Methods in Enzymology, Vol. 612: High-Density Sequencing Applications in Microbial Molecular Genetics (Editor: A.J. Carpoussis), Elsevier, San Diego, pp. 147-181, (2018). PMID: 30502940

He, F., Amrani, N., Johansson, M.J.O., and Jacobson, A. Qualitative and quantitative assessment of the activity of the yeast NMD pathway. In: Methods in Enzymology-RNA Turnover (Editors: L. Maquat and M. Kiledjian), Elsevier, San Diego, pp.127-147. (2008). PMID: 19215756.

He, F. and Jacobson, A. Endogenous substrates of the yeast NMD pathway. In: Nonsense-mediated mRNA decay (Ed: LE Maquat), Landes Bioscience, pp. 27-41. (2006).

Peltz, S. W., Trotta, C., He, F., Brown, A., Donahue, J.L., Welch, E., and Jacobson, A. Identification of the cis-acting sequences and trans-acting factors involved in nonsense-mediated mRNA decay. Springer-Verlag. Vol. H71:1-10. (1993).