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Daniel R. Schoenberg


Office: 176 Rightmire Hall
Lab: 140 Rightmire Hall

Phone: (614) 688-3012
Lab: (614) 688-3448


PhD - University of Wisconsin
Postdoctoral Work - Baylor College of Medicine

Dr. Schoenberg is Director of the Ohio State University Center f​or RNA Biology.

The Schoenberg lab focuses on post-transcriptional control of gene expression through changes in mRNA translation, modification and decay. They were the first to show that mRNAs can be degraded by endonuclease cleavage and identified the first mRNA endonuclease, PMR1. They were also the first to identify cis-acting sequences that regulate poly(A) tail length, and in doing so showed that mRNAs with short poly(A) tails are as stable and well translated as mRNAs with longer poly(A) tails. The current focus of the lab is on cytoplasmic capping and cap homeostasis, processes that maintain integrity of the transcriptome and expand transcriptome and proteome complexity.

The discovery of cytoplasmic capping

The degradation of nonsense-containing b-globin mRNA in the cytoplasm of erythroid cells results in the accumulation of a series of metastable decay intermediates. A previous report described the 5’ ends of these fragments as having a cap or cap-like structure, but this seemed implausible because mRNA capping was thought to be restricted to the nucleus. In addition, loss of the cap was generally thought to be irreversible, leading immediately to mRNA decay. We knew that the decay products are generated in the cytoplasm and a search for cytoplasmic capping activity led to the identification of a cytoplasmic population of capping enzyme that resides in complex containing a kinase that converts RNA with a 5’-monophosphate end to a 5’-diphosphate substrate for capping and a methyltransferase that acts on recapped transcripts to restore a functional cap structure.

The cytoplasmic capping complex

Understanding the process of cytoplasmic capping requires knowing the proteins that carry out this process. Cytoplasmic capping is carried out by a complex of enzymes that perform sequential steps in a pathway, also known as a ‘metabolon’. The cytoplasmic capping complex assembles on Nck1, a protein with 3 SH3 domains and a C-terminal SH2 domain (see figure) that is best known as an adapter protein that functions in transducing receptor tyrosine kinase signaling. The cytoplasmic pool of capping enzyme is the result of its shuttling between the nucleus and cytoplasm, where it binds to the third SH3 domain of Nck1. The 5’ kinase binds to the second SH3 domain, and a methyltransferase currently under study rounds out the core proteins of the complex. Current projects seek to identify and characterize additional proteins of this complex and how it is regulated.

The importance of cytoplasmic capping

Cytoplasmic capping targets are not random, and the cycling of these mRNAs between capped and uncapped states provides a window into their protein products. Uncapped forms of recapping targets retain their poly(A) tails and accumulate in non-translating mRNP complexes. Thus recapping is all that is needed to restore these mRNAs to the translating pool. Recapped ends map to the transcription start site and to locations within the body of the mRNA. Many of these lie upstream of potential translation start sites and work in progress will map the precise locations of recapped ends and determine the impact of recapping on proteome complexity. Cytoplasmic capping has the potential to impact numerous processes and provide new insights into normal cell physiology and its disregulation in disease.

A video describing work in the Schoenberg lab as well as information about how you can contribute to supporting this work can be found on the Benefunder web site.​


Click here for a list of Publications:

Recent papers:

  • Kiss, D.L., Oman, K., Dougherty, J.A., Mukherjee, C., Bundschuh, R. and Schoenberg, D.R. (2016) Cap Homeostasis is Independent of Poly(A) Tail Length. Nucleic Acids Research, 44:304-14.
  • Kiss, D.L., Oman, K., Bundschuh, R. and Schoenberg, D.R. (2015) Uncapped 5’ Ends of mRNAs Targeted by Cytoplasmic Capping Map to the Vicinity of Downstream CAGE Tags. FEBS Letters 589:279-284.
  • Mukherjee, C., Bakthavachalu, B. and Schoenberg, D.R. (2014) The Cytoplasmic Capping Complex Assembles on Adapter Protein Nck1 bound to the Proline-rich C-terminus of Mammalian Capping Enzyme. PLoS Biology 12: e1001933.
  • Wein, N., Vulin, A., Falzarano, M.S., Al-Khalili Szigyarto, C., Maiti, B., Findlay, A., Heller, K.N., Uhlén, M,, Bakthavachalu, B., Messina, S., Vita, G., Passarelli, C., Gualandi, F., Wilton, S.D., Rodino-Klapac, L., Yang, L., Dunn, D.M., Schoenberg, D., Weiss, R.B., Howard, M.T., Ferlin,i A., Flanigan, K.M., (2014) A Novel IRES Identified In DMD Results In A Functional N-Truncated Dystrophin, Providing A Potential Route To Therapy For Patients With 5' Mutations. Nature Medicine 20: 992-1000.
  • Mascarenhas, R., Dougherty, J.A. and Schoenberg, D.R. (2013) SMG6 Cleavage Generates Metastable Decay Intermediates From Nonsense-Containing β-globin mRNA. PLoS One 8: e74791.
  • Mukherjee, C., Patil, D.P., Kennedy, B.A., Bakthavachalu, B., Bundschuh, R. and Schoenberg, D.R. (2012) Identification of Cytoplasmic Capping Targets Reveals a Role for Cap Homeostasis in Translation and mRNA Decay. Cell Reports, 2: 674-684.
  • Gu, S.-Q., Bakthavachalu, B., Han, J., Patil, D.P., Otsuka, Y., Guda, C. and Schoenberg, D.R. (2012) Identification of the Human PMR1 mRNA Endonuclease as an Alternatively Processed Product of the Gene for Peroxidasin-Like Protein. RNA 18: 1186-1196.
  • Schoenberg, D.R. and Maquat, L.E. (2012) Regulation of Cytoplasmic mRNA Decay. Nature Reviews Genetics, 13: 246-259.
  • Rajaram, M.V.S., Nib, B., Morris, J.D., Brooks, M.N., Carlson, T.K., Bakthavachalu, B. Schoenberg, D.R., Torrelles, J.B. and Schlesinger, L.S. (2011) M. tuberculosis Lipomannan Blocks TNF Biosynthesis by Regulating Macrophage MAPK-Activated Protein Kinase 2 (MK2) and miR125b. Proceedings of the National Academy of Sciences USA 108: 17408-17423. Cited in Faculty of 1000. http://f1000.com/13357259​
  • Schoenberg, D.R. (2011) Mechanisms of Endonuclease-mediated mRNA Decay. Wiley Interdisciplinary Reviews: RNA 2: 582-600. DOI:10.1002/wrna.78.
  • Nechama, M., Peng, Y., Bell, O., Briata, P., Gherzi, R., Schoenberg, D. and Naveh-Many, T. (2009) KSRP-PMR1-exosome Interactions Determine Parathyroid Hormone mRNA Levels and Stability in Transfected Cells. BMC Cell Biology, 10:70.
  • Kolb, S.J., Sutton, S. and Schoenberg, D.R. (2010) RNA Processing Defects Associated with Diseases of the Motor Neuron. Muscle and Nerve 41: 5-17.
  • Schoenberg, D.R. and Maquat, L.E. (2009) Re-capping the Message. Trends in Biochemical Sciences 34: 435-442.