Our lab studies the cellular architecture and regulation of protein synthesis, with a primary focus on understanding how cells regulate both the subcellular location and temporal dynamics of protein synthesis. Here, we focus on mRNA localization. mRNA localization is a primary mechanism used by all eukaryotic cells to regulate the spatiotemporal component of gene expression - where and when an mRNA is translated to yield its encoded protein. Such regulation is critical for proper control of cell dynamics, cell signaling and cell division. Of the many mRNA localization phenomena that have been identified to date, the most prominent is mRNA localization to the endoplasmic reticulum (ER). mRNA localization to the ER is distinguished by its magnitude (ca. 30-40% of the mRNA transcriptome is localized to the ER) and temporal demands - all newly exported mRNAs undergo selection for translation in the cytosol and/or ER compartments.
   In studying this question, we use a broad array of tools drawn from biochemistry, cell biology, genomics, and computational biology, and are focusing on several related themes that define this central question. Primarily, we are working to establish the rules that govern the association of mRNAs with the ER. One mechanism, in which a signal in the encoded protein leads to recruitment to the ER, has been described. The identification and characterization of additional pathways leading to ER enrichment remains a central and largely unanswered question. We are also investigating how mRNAs might directly bind to the ER independently of their association with ribosomes. In a recent paper from our lab, we have demonstrated that the mRNAs that encode the resident proteins of the endomembrane system (nuclear envelope, ER, Golgi, lysosomes, peroxisomes and plasma membrane) are localized to discrete domains of the ER and undergo direct binding interactions with components of the ER membrane components. We are keenly interested in understanding what signals and signal binding protein(s) direct this critical subset of mRNAs to this discrete subcellular location in the cell and how such localization contributes to the biogenesis of cell structure and regulation of cell function.

E-mail
c.nicchitta@cellbio.duke.edu

436A Nanaline Duke Bldg., Box 3709
Duke University Medical Center
Durham, NC 27710

Telephone
919-684-8948 (office)
919-684-8980 (lab)
Fax 919-684-5481

Nicchitta Lab Site

Selected Publications
Reid DW, Nicchitta CV. (2011) Genome-scale ribosome footprinting identifies a primary role for endoplasmic reticulum-bound ribosomes in the translation of the mRNA transcriptome. J Biol Chem. 2011 Dec 23. [in press]

Chen Q, Jagannathan S, Reid DW, Zheng T, Nicchitta CV. (2011) Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells. Mol Biol Cell. 22(14):2646-58. -PDF-

Jagannathan S, Nwosu C, Nicchitta CV. (2011) Analyzing mRNA localization to the endoplasmic reticulum via cell fractionation. Methods Mol Biol. 2011;714:301-21. -PDF-

Pyhtila B, Zheng T, Lager PJ, Keene JD, Reedy MC, Nicchitta CV. (2008) Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum. RNA. 14(3):445-53. -PDF-

Stephens SB, Nicchitta CV. (2008) Divergent regulation of protein synthesis in the cytosol and endoplasmic reticulum compartments of mammalian cells. Mol Biol Cell. 19(2):623-32. -PDF-

Lerner RS, Nicchitta CV. (2006) mRNA translation is compartmentalized to the endoplasmic reticulum following physiological inhibition of cap-dependent translation. RNA. 12(5):775-789. -PDF-

Stephens, S.B., Dodd, R.D., Brewer, J.W., Lager, P.J., Keene, J.D., and Nicchitta, CV. (2005) Stable Ribosome Binding to the Endoplasmic Reticulum Enables Compartment-Specific Regulation of mRNA Translation. Mol. Biol. Cell 16(12):5819-31. -PDF-

Nicchitta, CV., Lerner, R.S., Stephens, S.B., Dodd, R.D., and Pyhtila, B. (2005) Pathways for compartmentalizing protein synthesis in eukaryotic cells: The Template Partitioning Model. Mol. Cell. Biochem. 83(6):687-695. -PDF-

Lerner, R.S., Seiser, R.M., Zheng, T., Lager, P.J., Reedy, M.C., Keene, J.D., Nicchitta, C.V. (2003) Partitioning and translation of mRNAs encoding soluble proteins on membrane-bound ribosomes. RNA. 9(9):1123-37.

Current Projects
Protein synthesis regulation:
  What role does protein synthesis play in the regulation of ribosome binding and release on the ER?
  How is the protein synthesis activity of ER-bound ribosomes regulated during normal and stress conditions?
  What is the mechanism of mRNA targeting to, and release from, the ER membrane?
  Do (subclasses of) mRNAs contain ER-directed localization information?

Chaperone Function:
  How are GRP94 interactions with polypeptide substrates regulated?
  What is the identity of the GRP94 "proteome"? (those proteins whose functional expression requires GRP94).
  How is GRP94 recognized by the cells of the immune system?