Publications – Choder lab

Key publications

1. Farago, M., Nahari, T., Hammel, C., Cole, C. N., and Choder, M. (2003). Rpb4p, a Subunit of RNA Polymerase II, Mediates mRNA Export during Stress. Mol. Biol. Cell 14, 2744-2755.
2. Lotan, R, Goler Bar-On, V., Harel-Sharvit, L., Duek, L., Melamed, D., and Choder, M. (2005). The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes & Dev. 19, 3004-3016.
3. Selitrennik, M., Duek, L, Lotan, R., and Choder, M. (2006). Nucleo-cytoplasmic shuttling of Rpb4 and Rpb7 subunits of yeast RNA polymerase II by two pathways. Eukaryotic Cell 5, 2092-2103.
4. Dori, D. and Choder, M. (2007). Conceptual modeling of biological systems: the mRNA lifecycle as a case in point. PLoS One, 2,e872.
5. Lotan, R., Goler Bar-On, V., Duek, L., Haimovitz, G., and Choder, M. (2007). The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J. Cell Biol. 178, 1133-1143.
  - See commentary by Leslie M. J. Cell Biol. 178, 1095 (2007).
  - Recommended by “Faculty of 1000″ (F1000.com/1119939)
6. Goler-Baron, V., Seletrinnik, M., Barkai, O., Haimovitz, G., Lotan, R., and Choder, M. (2008). Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes & Dev.22, 2022-2027.
7. Harel-Sharvit, L., Eldad, N., Haimovich, G., Barkai, O., Duek, L. and Choder, M. (2010). RNA polymerase II subunits link transcription and mRNA decay to translation. Cell 143, 552-563.
  - Selected for the Journal “Leading Edge Preview” see Preker, P and Heick Jensen, T. (2010). Translation by remote control. Cell 143, 501-502.
  - Selected for “Research Highlight” in Nature Reviews | Mol Cell Biol. See Skinner, M (2011). Protein synthesis: An expressive couple. Nat. Rev. Mol Cell Biol. 12, 8.
  - Recommended by “Faculty of 1000″ (http://f1000.com/6339956).
8. Choder, M. (2011). mRNA imprinting: additional level in the regulation of gene expression. Cellular Logistics 1, 37-40.
9. Shalem, O., Groisman, B., Choder, M., Dahan O., and Pilpel, Y. (2011) Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II. PLoS Genet 7(9): e1002273.
10. Bregman, A., Avraham-Kelbert, M., Barkai, O., Duek, L., Guterman, A., and Choder, M. Promoter elements regulate cytoplasmic mRNA decay. (2011). Cell, 147, 1473-83.
  - Selected for the Journal “Leading Edge Preview” see Bellofatto, V. and Wilusz, J. (2011). Transcription and mRNA stability: parental guidance suggested. Cell 147, 1438-9.
  - Selected for “Research Highlight” in Nat Rev Mol Cell Biol. 13, 65
  - Selected for “Research Highlight” in Nature Reviews | Genetics. Nat Rev Genet. 13, 72.
  - Recommended by “Faculty of 1000″ (“top 2%”) (http://f1000.com/13485010).
11. Somech, Y., Choder, M., and Dori, D. Conceptual Model-Based Systems Biology: Mapping Knowledge and Discovering Gaps in the mRNA Transcription Cycle. PLoS One 7, e51430.
12. Haimovich, G., Medina, A.D., Causse, S.Z., Garber, M., Millán-Zambrano, G., Barkai, O., Chávez, S., Pérez-Ortín, J.E., Darzacq, X., and Choder, M. (2013). Gene expression is a circular: factors for mRNA degradation also foster mRNA synthesis. Cell, 153, 1000-1011.
13. • Selected for “Research Highlight” in Nature Reviews | Genetics
  See Muers, M. (2013). mRNA decay factors regulate transcription. Nature Reviews Genetics 14, 444 doi:10.1038/nrg3530.
  • Recommended by “Faculty of 1000” (“top 2%”) http://f1000.com/prime/718042734?subscriptioncode=806f4e25-1910-4cf1-be82-d86b22bb8786
14. Medina DA, Jordán-Pla A, Millán-Zambrano G, Chávez S, Choder M, Pérez-Ortín JE. (2014). Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast. Front Genet I Non-Coding RNA. 5, 1-10. doi: 10.3389/fgene.2014.00001. eCollection 2014.
15. Somekh, J., Haimovich, G., Guterman, A. Dori, D., and Choder, M. (2014). Conceptual Modeling of mRNA Decay Provokes New Hypotheses. PLoS One, e107085. doi:10.1371/journal.pone.0107085.
16. Aronov, S., Dover, S., Suss-Toby, E, Shmoish, M., Duek, L., and Choder, M. (2015). Pheromone-encoding mRNA is transported to the yeast mating projection by specific RNP granules. J. Cell Biol., 209, 829-842.
17. Duek, L., Barkai, O., Elran, R., Adawi, I., and Choder, M. (2018). Dissociation of Rpb4 from RNA polymerase II is important for yeast functionality. PLoS One https://doi.org/10.1371/journal.pone.0206161.
18. Blasco-Moreno, B., de Campos-Mata, L., Böttcher, R., García-Martínez, J., Jungfleisch, J., Nedialkova, D.D., Chattopadhyay, S., Gas, M.E., Oliva, B., Pérez-Ortín, J.E., Leidel, S.A., Choder, M.*, Díez, J.* (2019). The exonuclease Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins. Nature communication 10,1298. doi: 10.1038/s41467-019-09199-6. * co-corresponding author.
19. Fischer, J, Song, Y.S., Nir Yosef, N., Julia di Iulio J., Churchman, S.L., and Choder, M. (2020). The yeast exonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast. J. Biol. Chem. 295, 11435–11454. https://doi.org/10.1016/j.celrep.2020.108578
20. Richard, S., Gross, L., Fischer, J., Bendalak, K., Tamar Ziv, T., Urim, S., and Choder, M. (2021). Numerous post-translational modifications of RNA polymerase II subunit Rpb4 link transcription to post-transcriptional mechanisms. Cell rep. 32, 108578 https://doi.org/10.1016/j.celrep.2020.108578
21. Chattopadhyay, S., Garcia-Martinez, J., Haimovich, G., Khwaja, A., Barkai, O., Ghosh, A., Gabriela-Chuarzman, S., Schuldiner, M., Elran, R., Rosenberg, M., Sloan Bohnsack, K., Sloan Bohnsack, M., Perez-Ortin, J.E., Choder, M. RNA-controlled Nucleocytoplasmic shuttling of the exoribonuclease Xrn1 is required for mRNA synthesis and decay and for responses to environmental changes. Nature communication 13(1), 7184-7201. doi: 10.1038/s41467-022-34417-z.
22. Kelbert, M, Jordan, T, de-Miguel-Jiménez, L, García-Martínez, J., Selitrennik, M., Guterman, A., Henig, N., Granneman S., Pérez-Ortín, J.E*. Chávez S.*, Choder, M.* (2024). The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis and cytoplasmic decay. eLife 12, RP90766 PMC11446548 https://doi.org/10.7554/eLife.90766.1
23. Shira Urim, Artyom Artamonov, Shubham Deshmukh, and Mordechai Choder. mRNA Imprinting: transcription apparatus can remotely control cytoplasmic post-transcriptional mechanisms by dozens of proteins. eLife, in press.
  Reviews
24. Choder, M. (2004). Rpb4 and Rpb7: subunits of RNA polymerase II and beyond. Trends Biochem Sci. (TiBS) 29, 674-681.
25. Dahan, N. and Choder, M. (2013). The transcriptional machinery regulates mRNA translation and decay in the cytoplasm. In BBA special issue entitled “The biochemistry and structural biology of RNA polymerase II transcript elongation”, Edited by Svejstrup, JQ. BBA 1829, 169-173.
26. Haimovich, G., Choder, M. Singer R., and Trcek, T. The linkage between mRNA synthesis and decay. In BBA Special issue on “RNA decay mechanisms”. In press.
27. Perez-Ortin, J.E., Alepuz, P., Chavez, S., and Choder, M. Regulation of eukaryotic gene expression by mRNA decay. Solicited by J. Mol. Biol. For a special issue on “Non-coding RNA in Systems”. In press.