A unique feature of T-cell receptor (TCR) and immunoglobulin (Ig) genes is that they undergo rearrangements during lymphocyte development. A consequence of these programmed mutational events is that approximately two thirds of the rearranged TCR and Ig genes are out of frame, and thus contain premature termination codons (PTCs). Studies have demonstrated that PTCs cause TCR and Ig mRNA levels to be dramatically downregulated. This process, termed nonsense codon-mediated downregulation (NMD), has been shown to depress of expression of deleterious truncated proteins, and thus it may be mediated by a surveillance mechanism that protects cells from dominant negative-mutant proteins. Interestingly, TCR and Ig transcripts are more strongly downregulated by the NMD mechanism than are other known mammalian transcripts, suggesting the possibility that rearranging genes which frequently acquire PTCs have evolved mechanisms to amplify the NMD response. Because nonsense codons are only known to be recognized by the cytoplasmic translational machinery, it was expected that NMD would occur in the cytoplasm. Unexpectedly, several lines of evidence suggest that NMD occurs in the nucleus of lymphoid cells, including the fact that an intron is required downstream of a nonsense codon to engage the downregulatory response. Further evidence for a role of the nucleus is the finding that nonsense codons increase the levels of alternatively spliced TCR transcripts that have excised the offending PTC.
The specific aims of this application are: (1) To explain the paradoxical effects of nonsense codons on nuclear-associated events. (2) To assess whether nonsense codon involves a translation- like mechanism (although a codon-induced event would normally be assumed to require translation, several lines of recent evidence suggest this might not be the case). (3) To identify the factors responsible for the robust downregulation of TCR and Ig mRNAs in response to PTCs. (4) To elucidate whether TCR and Ig mRNAs harboring PTCs are downregulated by a common mechanism that differs from that which acts on other mammalian transcripts. The study of NMD will contribute significantly to our understanding of the immune system. Elucidation of how nonsense codons regulate nuclear events may alter prevailing views of gene expression and its compartmentalization in eukaryotic cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM058595-04S1
Application #
6698233
Study Section
Allergy and Immunology Study Section (ALY)
Program Officer
Rhoades, Marcus M
Project Start
1999-01-01
Project End
2003-07-06
Budget Start
2002-01-01
Budget End
2003-07-06
Support Year
4
Fiscal Year
2003
Total Cost
$116,089
Indirect Cost
Name
University of Texas MD Anderson Cancer Center
Department
Microbiology/Immun/Virology
Type
Other Domestic Higher Education
DUNS #
800772139
City
Houston
State
TX
Country
United States
Zip Code
77030
Goetz, Alexandra E; Wilkinson, Miles (2017) Stress and the nonsense-mediated RNA decay pathway. Cell Mol Life Sci 74:3509-3531
Jones, Samantha H; Wilkinson, Miles (2017) RNA decay, evolution, and the testis. RNA Biol 14:146-155
Borgmann, Jennifer; Tüttelmann, Frank; Dworniczak, Bernd et al. (2016) The human RHOX gene cluster: target genes and functional analysis of gene variants in infertile men. Hum Mol Genet :
Lou, Chih H; Shao, Ada; Shum, Eleen Y et al. (2014) Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Rep 6:748-64
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Liu, Chen; Karam, Rachid; Zhou, YingQi et al. (2014) The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nat Med 20:596-8
Lasalde, Clarivel; Rivera, Andrea V; León, Alfredo J et al. (2014) Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1. Nucleic Acids Res 42:1916-29
Karam, Rachid; Wengrod, Jordan; Gardner, Lawrence B et al. (2013) Regulation of nonsense-mediated mRNA decay: implications for physiology and disease. Biochim Biophys Acta 1829:624-33
Ramaiah, Madhuvanthi; Shum, Eleen Y; Wilkinson, Miles F (2012) How to activate a gene: decap its associated noncoding RNA. Mol Cell 45:271-3
Karam, Rachid; Wilkinson, Miles (2012) A conserved microRNA/NMD regulatory circuit controls gene expression. RNA Biol 9:22-6

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