Publications – Choder lab

Choder, M. (1991). A general topoisomerase I-dependent transcriptional repression in the stationary-phase in yeast. Genes & Dev. 5,2315-2326.
Choder, M. (1993). A growth limiting mechanism in the last growth phase of the yeast life cycle involves RPB4, a subunit of RNA polymerase II. J. Bacteriol. 175, 6358-6363.
Choder, M. and Young, R. A. (1993). A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol. Cell. Biol. 13, 6984-6991.
Weisman, R. Choder, M., and Koltin Y. (1997). Rapamycin specifically interferes with the developmental response of fission yeast to starvation. J. Bacteriol. 179, 6325-6334.
Rosenheck, S., and Choder, M. (1998). Rpb4, a subunit of RNA polymerase II, enables the enzyme to transcribe at temperature extremes in vitro. J. Bacteriol. 180, 6187-6192.
Shefer, A., Varon, M., and Choder, M. (1999). Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol. Cell. Biol. 19, 2672-2680.
Meunier, J-R., and Choder, M. (1999). Saccharomyces cerevisiae colony growth and ageing: biphasic growth accompanied by changes in gene expression and colony morphology. Yeast, 15, 1159-1170.
Paz, I. Abramovitz, L., and Choder, M. (1999). Starved Saccharomyces cerevisiae cells have the capacity to support internal initiation of translation. J. Biol. Chem. 274, 21741-21745.
Paz, I., Meunier, J-R., and Choder, M. (1999). Monitoring dynamics of gene expression in yeast during stationary phase. Gene, 236, 33-42.
Jona, G., Choder, M., and Gileadi, O. (2000) Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochem. Biophys. Acta 1491, 37-48.
Varon, M., and Choder, M. (2000). Organization and cell-cell interaction in starved Saccharomyces cerevisiae colonies. J. Bacteriol.182, 3877-3880. A photograph from this paper is presented as a cover picture.
Weisman, R., and Choder, M. (2001). The S. pombe TOR homologue, tor1+, is required for sexual development, entrance into stationary phase and responses to stress conditions. J. Biol. Chem. 276, 7027-7032.
Weizman, R., Finkelstein, S. and Choder, M. (2001). Rapamycin blocks sexual development in fission yeast through inhibition of FKBP12 homolog. J. Biol. Chem. 276, 24736-24742
Paz, I. and Choder, M. (2001). Eukaryotic translation initiation factor 4E-dependent translation is not essential for survival of starved yeast cells. J. Bacteriol. 183, 4477-4483.
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.
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.
Topaz, O., Indelman, M., Chefetz, I., Geiger, D., Metzker, A., Altschuler, Y., Choder, M., Bercovich, D., Uitto, J., Bergman, R., Richard, G., and Sprecher, E. (2006). A Deleterious Mutation in SAMD9 causes Normophosphatemic Familial Tumoral Calcinosis. American Journal of Human Genetics 79, 759-764.
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.
Dori, D. and Choder, M. (2007). Conceptual modeling of biological systems: the mRNA lifecycle as a case in point. PLoS One, 2,e872.
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)

Mandel, H., Shemer, R., Zvi U. Borochowitz, Z. U., Okopnik, M., Knopf, C., Indelman, M., Drugan, A., Dov Tiosano, D., Gershoni, R.,Choder, M., and Sprecher, E. (2008). Female sex reversal with dysgenesis of kidneys, adrenals and lungs (SERKAL syndrome): a novel autosomal recessive disorder caused by ahomozygous loss-of-function mutation in WNT4. American Journal of Human Genetics 82, 39-47.
Nousbeck, J. Spiegel, R., Ishida-Yamamoto, A., Indelman, M., Shani-Adir, A., Adir, N., Lipkin, E., Bercovici, S., Geiger, D., van Steensel, M. A. Steijlen, P. M.,. Bergman, R., Bindereif, A., Choder, M., Shalev, S. Sprecher, E. (2008). Alopecia, Neurological defects and Endocrinopathy (ANE) syndrome caused by decreased expression of RBM28, a nucleolar protein associated with ribosome biogenesis. American Journal of Human Genetics 82, 1114-21.
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.
Wasserman T, Katsenelson K, Daniliuc S, Hasin T, Choder, M., and Aronheim A. (2010). A novel c-Jun N-terminal kinase (JNK)-binding protein WDR62 is recruited to stress granules and mediates a nonclassical JNK activation. Mol. Biol. Cell. 21,117-30.
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).

Choder, M. (2011). mRNA imprinting: additional level in the regulation of gene expression. Cellular Logistics 1, 37-40.
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.
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).
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.
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.
• 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
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.
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.
41. 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.
Bolshchikov, S., Somekh, J., Mazor, S., Wengrowicz, N., Choder, M., and Dori, D. (2015). Cognition-Based Visualization of the Dynamics of Conceptual Models: The Vivid OPM Scene Player. Systems Engeneering 18, 431-440. doi: 10.1002/sys.21321.
43. 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.
44. 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.
45. 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
46. 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
47. 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. Under review. Posted on bioRxiv doi: https://doi.org/10.1101/2021.04.01.437949.

Reviews

Choder, M. (2004). Rpb4 and Rpb7: subunits of RNA polymerase II and beyond. Trends Biochem Sci. (TiBS) 29, 674-681.
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.
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.
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.