Co-regulated expression of alpha and beta mRNAs encoding HLA-DR surface heterodimers is mediated by the MHCII RNA operon

Nucleic Acids Research

Volumn 41, Issue 6, 2013, Pages 3772-3786

  Pisapia, Laura ^a   Cicatiello, Valeria ^a   Barba, Pasquale ^a   Malanga, Donatella ^b   Maffei, Antonella ^a,c   Hamilton, Russell S ^d   Del Pozzo, Giovanna ^a  

^a INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

^b UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^c NewYork Presbyterian Hospital   (United States)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HETERODIMER; HLA DR ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MESSENGER RNA; RIBONUCLEOPROTEIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALPHA CHAIN; ARTICLE; BETA CHAIN; HUMAN; HUMAN CELL; IMMUNOSURVEILLANCE; MOLECULAR DOCKING; OPERON; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; RNA PROCESSING; RNA TRANSCRIPTION;

5' UNTRANSLATED REGIONS; ADAPTOR PROTEINS, SIGNAL TRANSDUCING; CELL LINE, TUMOR; DNA, COMPLEMENTARY; GENE EXPRESSION REGULATION; HLA-DR ALPHA-CHAINS; HLA-DR ANTIGENS; HLA-DR BETA-CHAINS; HUMANS; MODELS, GENETIC; NUCLEAR FACTOR 90 PROTEINS; NUCLEOTIDE MOTIFS; PROTEIN MULTIMERIZATION; RIBONUCLEOPROTEINS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA-BINDING PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84876042916     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt059     Document Type: Article

References (38)

1. Cresswell, P. (1994) Assembly, transport, and function of MHC class II molecules. Annu. Rev. Immunol., 12, 259-293.
2. Villadangos, J.A., Schnorrer,P. and Wilson, N.S. (2005) Control of MHC class II antigen presentation in dendritic cells: a balance between creative and destructive forces. Immunol. Rev., 207, 191-205.
3. Viret,C. and Janeway, C.A. Jr (1999) MHC and T cell development. Rev. Immunogenet., 1, 91-104.
4. Steimle, V., Siegrist, C.A., Mottet, A., Lisowska-Grospierre,B. and Mach, B. (1994) Regulation of MHC class II expression by interferon-gamma mediated by the transactivator gene CIITA. Science, 265, 106-109.
5. Guardiola,J. and Maffei, A. (1993) Control of MHC class II gene expression in autoimmune, infectious, and neoplastic diseases. Crit. Rev. Immunol., 13, 247-268.
6. Ting, J.P. and Trowsdale, J. (2002) Genetic control of MHC class II expression. Cell, 109(Suppl), S21-S33.
7. Corso, C., Pisapia, L., Citro, A., Cicatiello, V., Barba, P., Cigliano, L., Abrescia, P., Maffei, A., Manco,G. and Del Pozzo, G. (2011) EBP1 and DRBP76/NF90 binding proteins are included in the major histocompatibility complex class II RNA operon. Nucleic Acids Res., 39, 7263-7275.
8. Barber, G.N. (2009) The NFAR's (nuclear factors associated with dsRNA): evolutionarily conserved members of the dsRNA binding protein family. RNA Biol., 6, 35-39.
9. Zhou, H., Mazan-Mamczarz, K., Martindale, J.L., Barker, A., Liu, Z., Gorospe, M., Leedman, P.J., Gartenhaus, R.B., Hamburger, A.W. and Zhang, Y. (2010) Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer. Nucleic Acids Res., 38, 3619-3631.
10. Shi, L., Godfrey, W.R., Lin, J., Zhao,G. and Kao, P.N. (2007) NF90 regulates inducible IL-2 gene expression in T cells. J. Exp. Med., 204, 971-977.
11. Zhang, Y., Wang, X.W., Jelovac, D., Nakanishi, T., Yu, M.H., Akinmade, D., Goloubeva, O., Ross, D.D., Brodie,A. and Hamburger, A.W. (2005) The ErbB3-binding protein Ebp1 suppresses androgen receptor-mediated gene transcription and tumorigenesis of prostate cancer cells. Proc. Natl Acad. Sci. USA, 102, 9890-9895.
12. Lessor, T.J., Yoo, J.Y., Xia, X., Woodford,N. and Hamburger, A.W. (2000) Ectopic expression of the ErbB-3 binding protein ebp1 inhibits growth and induces differentiation of human breast cancer cell lines. J. Cell. Physiol., 183, 321-329.
13. Soutoglou,E. and Talianidis, I. (2002) Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science, 295, 1901-1904.
14. Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25, 402-408.
15. Vashist, S., Bhullar,D. and Vrati, S. (2011) La protein can simultaneously bind to both 3′-and 5′-noncoding regions of Japanese encephalitis virus genome. DNA Cell Biol., 30, 339-346.
16. Havgaard, J.H., Torarinsson,E. and Gorodkin, J. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908.
17. Del Pozzo, G., Ciullo, M., Autiero,M. and Guardiola, J. (1994) Control of nucleo-cytoplasmic HLA-DRA mRNA partitioning by interaction of a retention signal with compartmentalized proteins. J. Mol. Biol., 240, 193-204.
18. Keene, J.D. (2007) RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet., 8, 533-543.
19. Mapendano, C.K., Lykke-Andersen, S., Kjems, J., Bertrand,E. and Jensen, T.H. (2010) Crosstalk between mRNA 3′ end processing and transcription initiation. Mol. Cell, 40, 410-422.
20. Nagaike, T., Logan, C., Hotta, I., Rozenblatt-Rosen, O., Meyerson,M. and Manley, J.L. (2011) Transcriptional activators enhance polyadenylation of mRNA precursors. Mol. Cell, 41, 409-418.
21. Garcia-Oliver, E., Garcia-Molinero,V. and Rodriguez-Navarro, S. (2012) mRNA export and gene expression: The SAGA-TREX-2 connection. Biochim. Biophys. Acta, 1819, 555-565.
22. Hao,S. and Baltimore, D. (2009) The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules. Nat. Immunol., 10, 281-288.
23. Mukherjee, N., Lager, P.J., Friedersdorf, M.B., Thompson, M.A. and Keene, J.D. (2009) Coordinated posttranscriptional mRNA population dynamics during T-cell activation. Mol. Syst. Biol., 5, 288.
24. Kiesler, P., Haynes, P.A., Shi, L., Kao, P.N., Wysocki, V.H. and Vercelli, D. (2010) NF45 and NF90 regulate HS4-dependent interleukin-13 transcription in T cells. J. Biol. Chem., 285, 8256-8267.
25. Vumbaca, F., Phoenix, K.N., Rodriguez-Pinto, D., Han, D.K. and Claffey, K.P. (2008) Double-stranded RNA-binding protein regulates vascular endothelial growth factor mRNA stability, translation, and breast cancer angiogenesis. Mol. Cell. Biol., 28, 772-783.
26. Pfeifer, I., Elsby, R., Fernandez, M., Faria, P.A., Nussenzveig, D.R., Lossos, I.S., Fontoura, B.M., Martin, W.D. and Barber, G.N. (2008) NFAR-1 and -2 modulate translation and are required for efficient host defense. Proc. Natl Acad. Sci. USA, 105, 4173-4178.
27. Zhang, Y., Woodford, N., Xia,X. and Hamburger, A.W. (2003) Repression of E2F1-mediated transcription by the ErbB3 binding protein Ebp1 involves histone deacetylases. Nucleic Acids Res., 31, 2168-2177.
28. Kuwano, Y., Pullmann,R. Jr, Marasa, B.S., Abdelmohsen, K., Lee, E.K., Yang, X., Martindale, J.L., Zhan,M. and Gorospe, M. (2010) NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif. Nucleic Acids Res., 38, 225-238.
29. Bose, S.K., Sengupta, T.K., Bandyopadhyay,S. and Spicer, E.K. (2006) Identification of Ebp1 as a component of cytoplasmic bcl-2 mRNP (messenger ribonucleoprotein particle) complexes. Biochem. J., 396, 99-107.
30. Squatrito, M., Mancino, M., Sala,L. and Draetta, G.F. (2006) Ebp1 is a dsRNA-binding protein associated with ribosomes that modulates eIF2alpha phosphorylation. Biochem. Biophys. Res. Commun., 344, 859-868.
31. Kim, C.K., Nguyen, T.L., Joo, K.M., Nam, D.H., Park, J., Lee, K.H., Cho, S.W. and Ahn, J.Y. (2010) Negative regulation of p53 by the long isoform of ErbB3 binding protein Ebp1 in brain tumors. Cancer Res., 70, 9730-9741.
32. Kowalinski, E., Bange, G., Bradatsch, B., Hurt, E., Wild,K. and Sinning, I. (2007) The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions. FEBS Lett., 581, 4450-4454.
33. Isken, O., Grassmann, C.W., Sarisky, R.T., Kann, M., Zhang, S., Grosse, F., Kao, P.N. and Behrens, S.E. (2003) Members of the NF90/NFAR protein group are involved in the life cycle of a positive-strand RNA virus. EMBO J., 22, 5655-5665.
34. Lunde, B.M., Moore,C. and Varani, G. (2007) RNA-binding proteins: modular design for efficient function. Nat. Rev. Mol. Cell. Biol., 8, 479-490.
35. Parrott, A.M., Walsh, M.R. and Mathews, M.B. (2007) Analysis of RNA:protein interactions in vivo: identification of RNA-binding partners of nuclear factor 90. Methods Enzymol., 429, 243-260.
36. Neplioueva, V., Dobrikova, E.Y., Mukherjee, N., Keene, J.D. and Gromeier, M. (2010) Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PLoS One, 5, e11710.
37. Lange, S.J., Maticzka, D., Mohl, M., Gagnon, J.N., Brown, C.M. and Backofen, R. (2012) Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res., 40, 5215-5226.
38. Doetsch, M., Schroeder,R. and Furtig, B. (2011) Transient RNA-protein interactions in RNA folding. FEBS J., 278, 1634-1642.