Publications
2024
Lee ES, Smith HW, Wang YE, Ihn SJ, Scalize de Olivera L, Kejiou NS, Liang YL,, Nabeel-Shah S, Jomphe RY, Pu S, Greenblatt JF, and Palazzo AF. N-6-methyladenosine (m6A) Promotes the Nuclear Retention of mRNAs with Intact 5’ Splice Site Motifs. Life Science Alliance (in press)
Qiu Y, Kang YM, Korfmann C, Pouyet F, Eckford A, and Palazzo AF. The GC-content at the 5’ends of human protein-coding genes is undergoing mutational decay. Genome Biology, 2024, 25:219. link
Ihn SJ, Farlam-Williams L, Palazzo AF*, and Lee HO*. Cytoplasmic protein-free mRNA induces stress granules by two G3BP1/2-dependent mechanisms. Submitted, preprint available at bioRxiv link. *Co-corresponding authors.
Yerlici VT, Astori A, Kejiou NS, Jordan CA, Khosraviani N, Chan JNY, Hakem R, Raught B, Palazzo AF, Mekhail K. SARS-CoV-2 targets ribosomal RNA biogenesis. Cell Repors, 2024, 43:113891. link
Palazzo AF, Qiu Y, and Kang YM, mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biology. 2024, 21(1):1-12. link
Li J, Su L, Jiang J, Wang YE, Ling Y, Qiu Y, Yu H, Wu J, Jiang S, Zhang T, Palazzo AF*, and Shen Q*. RanBP2/Nup358 Mediates Sumoylation of STAT1 and Antagonizes Interferon-α-Mediated Antiviral Innate Immunity. International Journal of Molecular Sciences, 2024, 25(1):299. *Co-corresponding author. link
Lee VW , Kam KQ, Mohamed AR, Musa H, Anandakrishnan P, Shen Q, Palazzo AF, Dale RC, Lim M, Thomas T. Defining the Clinicoradiologic Syndrome of SARS-CoV-2 Acute Necrotizing Encephalopathy. Neurol Neuroimmunol Neuroinflamm. 2024 11(1):e200186. link
2023
Gouy B, Decorsière D, Desgraupes S, Duan W, Ouyang H, Wang YE, Yeh A, Palazzo AF, Moraes TJ, Nisole S, and Arhel NJ. Rapid and inexpensive bedside diagnosis of RAN binding protein 2-associated acute necrotizing encephalopathy. Frontiers in Neurology, 2023, 14:1282059. link
Kejiou NS, Ilan L, Aigner S, Luo E, Tonn T, Ozadam H, Lee M, Cole GB, Rabano I, Rajakulendran N, Yee BA, Najafabadi HS, Moraes TF, Angers S, Yeo GW, Cenik C, Palazzo AF. Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling. Nucleic Acid Research, 2023, 51(21):6461-6478. link
2022
Havstad J, and Palazzo AF. Not functional yet a difference maker: Junk DNA as a case study. Biology & Philosophy, 2022, 37:29. link
Bley CJ, Nie S, Mobbs GW, Petrovic S, Gres AT, Liu X, Mukherjee S, Harvey S, Huber FM, Lin DH, Brown B, Tang AW, Rundlet EJ, Correia AR, Chen S, Regmi SG, Stevens TA, Jette CA, Dasso M, Patke A, Palazzo AF, Kossiakoff AA, and Hoelz A. Architecture of the cytoplasmic face of the nuclear pore. Science, 2022, 376(6598). link
Palazzo AF, Joseph J, Lim M, Thakur KT. Workshop on RanBP2/Nup358 and acute necrotizing encephalopathy. Nucleus, 2022, 13(1):154-169. link
Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, and Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5’ splice site motifs within nuclear speckles. RNA, 2022, 28(6):878-894. link
Jiang J, Wang YE, Palazzo AF, Shen Q. Roles of nucleoporin RanBP2/Nup358 in acute necrotizing encephalopathy type 1 (ANE1) and viral infection. International Journal of Molecular Sciences, 2022, 23:3548. link
Palazzo AF. and Kejiou NS. Non-Darwinian Molecular Biology. Frontiers in Genetics, 2022, 13:831068. link
2021
Shen Q, Wang YE, Palazzo AF. Crosstalk between nucleocytoplasmic trafficking and the innate immune response to viral infection. Journal of Biological Chemistry, 2021, 297(1):100856, doi: 10.1016/j.jbc.2021.100856. link
Go CD, Knight JDR, Rajasekharan A, Rathod B, Hesketh GG, Abe KT, Youn JY, Samavarchi-Tehrani P, Zhang H, Zhu LY, Popiel E, Lambert JP, Coyaud É, Cheung SWT, Rajendran D, Wong CJ, Antonicka H, Pelletier L, Palazzo AF, Shoubridge EA, Raught B, Gingras AC. A proximity-dependent biotinylation map of a human cell. Nature, 2021, 595(7865):120-124. link
Shen Q, Wang YE, Truong M, Mahadevan K, Wu JJ, Zhang H, Li J, Smith HW, Smibert CA, Palazzo AF. RanBP2/Nup358 enhances miRNA activity by sumoylating Argonautes. PLOS Genetics, 2021, 17(2):e1009378. link
Palazzo AF. and Kang YM. GC-content biases in protein-coding genes act as an "mRNA identity" feature for nuclear export. Bioessays, 2021, 43(2):e2000197. link
2020
Palazzo AF. and Koonin, EV. Functional Long Non-coding RNAs Evolve from Junk Transcripts. Cell, 2020, 183(5):1151-1161. link
Lee, ES, Wolf, E, Ihn, SJ, Smith, H, Emili, A and Palazzo AF. TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes. Nucleic Acid Research, 2020 48(20):11645-11663. link
Wu, JJ and Palazzo, AF. Visualization of Endoplasmic Reticulum-Associated mRNA in Mammalian Cells. Methods Mol Biol., 2020 2166:35-49. link
Linquist, S., Doolittle, W.F. and Palazzo, A.F. Getting clear about the F-word in genomics. PLoS Genetics, 2020 16(4): e1008702. link
Wolf, E.J., Miles, A. Lee, E.S., Nabeel-Shah, S., Greenblatt, J.F., Palazzo, A.F., Tropepe, V., and Emili, A. MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development. Cell Reports, 2020 31(8):107693. link
2018
Chan JTH, Liu Y, Khan S, St-Germain JR, Zou C, Leung LYT, Yang J, Shi M, Grunebaum E, Campisi P, Propst EJ, Holler T, Bar-Or A, Wither JE, Cairo CW, Moran MF, Palazzo AF, Cooper MD, Ehrhardt GRA. A tyrosine sulfation-dependent HLA-I modification identifies memory B cells and plasma cells. Science Advances 2018 4(11):eaar7653.
Palazzo, A.F., and Lee, E.S. Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs, 2018 Frontiers in Genetics, 2018, 9 (440):1-16.
2017
Voigt, F., Zhang, H., Cui, X.A., Liu, X.A, Eglinger, J., Lee, E.S., Chao, J.A. and Palazzo, A.F. Single-molecule quantification of translation-dependent association of mRNAs with the endoplasmic reticulum. Cell Reports, 2017, 21:3740-53.
Lee, E.S. and Palazzo, A.F. Assessing mRNA nuclear export in mammalian cells by microinjection. Methods, 2017, 126:76-85.
Kejiou, N. and Palazzo, A.F. mRNA Localization as a Rheostat to Regulate Subcellular Gene Expression. WIREs RNA, 2017 e1416.
Cenik, C., Chua, H.N., Singh, G., Akef, A., Snyder, M., Palazzo, A.F., Moore, M.J., and Roth, F. A A Common Class of Transcripts with 5'-Intron Depletion, Distinct Early Coding Sequence Features, and N1-Methyladenosine Modification. RNA, 2017 23:270-83.
2016
Palazzo, A.F. and Truong, M. Single particle imaging of mRNAs crossing the nuclear pore: surfing on the edge. Bioessays, 2016 38(8):744-50.
2015
Akef, A., Lee, E.S. and Palazzo, A.F. Splicing promotes the nuclear export of β-globin mRNA by overcoming nuclear retention elements. RNA, 2015 21(11):1908-20.
Cui, X.A., Zhang, H, Ilan, L, Liu, A.X., Kharchuk, I., and Palazzo, A.F. mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic rhgeticulum. Journal of Cell Science, 2015 128(18):3398-410
Lee, E.S., Akef, A., Mahadevan K., and Palazzo, A.F. The consensus 5’ splice site motif inhibits mRNA nuclear export. PLoS One, 2015 10 (3):e0122743.
Palazzo, A.F. and Lee, E.S. Non-coding RNA: what is functional and what is junk? Frontiers in Genetics, 2015 6(2):1-11.
2014
Zhang, H, Mahadevan, K and Palazzo, A.F. Sumoylation is Required for the Cytoplasmic Accumulation of a Subset of mRNAs Genes, 2014 5(4):982-1000.
Palazzo, A.F. and Gregory, R.T. The Case for Junk DNA. PLoS Genetics, 2014 10(5): e1004351. doi:10.1371/journal.pgen.1004351.
Cui, X.A. and Palazzo, A.F. Localization of mRNAs to the Endoplasmic Reticulum. WIREs RNA, 2014 5(4):481-92.
2013
Mahadevan, K., Zhang, H., Akef A., Cui, X.A., Gueroussov S., Cenik, C., Roth F.P. and Palazzo, A.F. RanBP2/Nup358 Potentiates the Translation of a Subset of mRNAs Encoding Secretory Proteins. PLoS Biology 2013, 11(4): e1001545.
Cui, X.A., Zhang, Y., Seo, J.H., and Palazzo, A.F. Identification of a region within the placental alkaline phosphatase mRNA that mediates p180-dependent targeting to the Endoplasmic Reticulum. Journal of Biological Chemistry, 2013 288(41):29633-29641.
Akef, A., Zhang, H., Masuda, S., and Palazzo, A.F. Trafficking of mRNAs containing ALREX-promoting elements through nuclear speckles. Nucleus, 2013, 4(4): 326-40.
Palazzo, A.F., Mahadevan, K., and Tarnawsky, S.P. ALREX-elements and introns: two identity elements that promote mRNA nuclear export. WIREs RNA, 2013, 4(5): 523-533.
2012
Cui, X.A. and Palazzo A.F. Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells. J Vis Exp. 2012, 70:e50066.
Cui, X.A., Zhang, H. and Palazzo A.F. p180 Promotes the Ribosome-Independent Localization of a Subset of mRNA to the Endoplasmic Reticulum. PLoS Biology 2012, 10(5):e1001336.
Tarnawsky, S.P., and Palazzo, A.F. Positional requirements for the stimulation of mRNA nuclear export by ALREX-promoting elements. Molecular BioSystems 2012, 8(10) 2527-2530.
Palazzo, A.F., and Akef, A. Nuclear Export as a Key Arbiter of “mRNA Identity” in Eukaryotes. Biochimica et Biophysica Acta 2012, 1819(6):566-77.
Palazzo, A.F., and Mahadevan, K. Alternative Splicing Rewires Cellular Metabolism to Turn on the Warburg Effect. Biomedical Research 2012, 23:SI 23-30.
2011
Cenik, C., Chua, H.N., Zhang, H, Tarnawsky, S., Akef, A., Derti, A., Tasan, M., Moore, M.J., Palazzo, A.F.*, and Roth, F.P.* Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS Genetics 2011, 7(4): e1001366. *co-corresponding authors.
2010
Gueroussov, S., Tarnawsky, S.P., Cui, X.A., Mahadevan, K. and Palazzo, A.F. Analysis of mRNA Nuclear Export Kinetics in Mammalian Cells by Microinjection. J Vis Exp. 2010, 46.
Alex Palazzo Publications, Pre-independent Researcher
Shibata, Y., Shemesh, T., Prinz, W.A., Palazzo, A.F., Kozlov, M.M.and Rapoport, T.A. Mechanisms determining the morphology of the peripheral ER. Cell. 2010, 143(5):774-88.
Palazzo, A.F., Springer, M., Shibata, Y., Lee, C.S., Dias, A.P. and Rapoport, T.A. The Signal Sequence Coding Region Promotes Nuclear Export of mRNA. PLoS Biol 2007, 5(12): e322.
Palazzo, A.F., Eng, C.H., Schlaepfer, D.D., Marcantonio, E.E. and Gundersen, G.G. Localized Stabilization of Microtubules by Integrin Facilitated Rho Signaling. Science 2004, 303:836-839.
Xiao D., Pinto J.T., Soh J.W., Deguchi A., Gundersen G.G., Palazzo A.F., Yoon J.T., Shirin H., Weinstein I.B. Induction of apoptosis by the garlic-derived compound S-allylmercaptocysteine (SAMC) is associated with microtubule depolymerization and c-Jun NH(2)-terminal kinase 1 activation. Cancer Res 2003, 63:6825-6837.
Palazzo A.F., Ackerman B. and Gundersen G.G. Tubulin acetylation and cell motility. Nature 2003, 421: 230.
Palazzo A.F. and Gundersen, G. G. Microtubule-actin crosstalk at focal adhesions Science Signaling 2002, 139:PE31.
Saucier C., Papavasiliou V., Palazzo A., Naujokas M.A., Kremer R. and Park M. Use of signal specific receptor tyrosine kinase oncoproteins reveals that pathways downstream from Grb2 or Shc are sufficient for cell transformation and metastasis Oncogene 2002, 21:1800-1811.
Yoon J.T., Palazzo A.F., Xiao D., DeloheryT.M., Warburton P.E., Bruce J.N., Thompson W.J., Sperl G., Whitehead C., Fetter J., Pamukcu R., Gundersen G.G. and Weinstein I.B. CP248, a derivative of exisulind, causes growth inhibition, mitotic arrest, and abnormalities in microtubule polymerization in glioma cells Mol Cancer Ther 2002, 1:393-404.
Palazzo A.F., Joseph H.L., Chen Y.J., Dujardin D.L., Alberts A., Pfister K.K., Vallee R.B. and Gundersen G.G. Cdc42, dynein and dynactin regulate MTOC reorientation independent of Rho-regulated microtubule stabilization Curr Biol 2001, 11: 1536-1541.
Palazzo A.F., Cook T.A., Alberts A. and Gundersen G.G. mDia mediates Rho-regulated formation and orientation of stable microtubules Nat Cell Biol 2001, 3: 723-729.
Yang H.C., Palazzo A., Swayne T.C. and Pon L.A. A retention mechanism for distribution of mitochondria during cell division in budding yeast Curr Biol 1999, 9:1111-1114.
Interviews and Profiles
04/23 Zimmer, C. What Cheetahs, Armadillos and Whales Revealed About Human DNA, New York Times.
06/22 Khan, R. Alex Palazzo: Drifting into molecular evolution, Unsupervised Learning Podcast.
08/18 Smith, K. The Palazzo Laboratory and ANE. Acute Necrotizing Awareness Day, ANE International.
03/15 Zimmer, C. Is Most of Our DNA Garbage? The New York Times Magazine.
05/14 Zimmer, C. The Case for Junk DNA. National Geographic – Phenomena: The Loom http://phenomena.nationalgeographic.com/2014/05/09/the-case-for-junk-dna/
08/12 Emerging Investigator Contributors 2012. Molecular BioSciences. 2012 8(10):2461-2465
01/11 Raper, V. Science Blogging and Tenure. Science Careers. 2011 doi: 10.1126/science.caredit.a1100007
2008 Williams, D. News from Departments, University of Toronto, Department of Biochemistry. CSBMCB Bulletin 2008. Page 84.
08/07 Wang, L. Friday Afternoons in the Lab. Chemical and Engineering News. 2007 85(34):88
05/07 Bonetta, L. Science enters the Blogosphere. Cell. 2007 129:443-445
09/06 Skipper, M., Would Mendel have been a blogger? Nature Reviews in Genetics. 2006 doi:10.1038/nrg1957